3K1A - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   INSIGHTS INTO SUBSTRATE BINDING AT FEMO-COFACTOR IN NITROGENASE FROM THE STRUCTURE OF AN ALPHA-70ILE MOFE PROTEIN VARIANT

Authors :   J. W. Peters, R. Sarma, B. M. Barney, S. Keable, L. C. Seefeldt, D. R. Dean

Date :   26 Sep 09 (Deposition) - 16 Feb 10 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.23

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Nitrogen Fixation, Mofe Protein, Nitrogenase, Isoleucine, Proton Reduction, Nitrogen, Acetylene, Hydride Reduction, Atp-Binding, Iron, Iron-Sulfur, Metal-Binding, Nucleotide- Binding, Oxidoreductase, Molybdenum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sarma, B. M. Barney, S. Keable, D. R. Dean, L. C. Seefeldt, J. W. Peters
Insights Into Substrate Binding At Femo-Cofactor In Nitrogenase From The Structure Of An Alpha-70(Ile) Mofe Protein Variant
J. Inorg. Biochem. V. 104 385 2010
PubMed-ID: 20022118 | Reference-DOI: 10.1016/J.JINORGBIO.2009.11.009

Molecule 1 - NITROGENASE MOLYBDENUM-IRON PROTEIN ALPHA CHAIN
	Chains	:	A, C
	EC Number	:	1.18.6.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NIFDK, NIFK
	Mutation	:	YES
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354
	Synonym	:	NITROGENASE COMPONENT I, DINITROGENASE

Molecule 2 - NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN
	Chains	:	B, D
	EC Number	:	1.18.6.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NIFD
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354
	Synonym	:	NITROGENASE COMPONENT I, DINITROGENASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CFN	2	Ligand/Ion	FE(7)-MO-S(9)-N CLUSTER
3	CLF	2	Ligand/Ion	FE(8)-S(7) CLUSTER
4	HCA	2	Ligand/Ion	3-HYDROXY-3-CARBOXY-ADIPIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:65 , ARG A:96 , GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , HOH A:497 , HOH A:498 , HOH A:505 , HOH A:516 , HOH A:530 , HOH A:590 , CFN A:6496	BINDING SITE FOR RESIDUE HCA A 494
2	AC2	SOFTWARE	ILE A:70 , ARG A:96 , HIS A:195 , TYR A:229 , CYS A:275 , GLY A:356 , GLY A:357 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:494	BINDING SITE FOR RESIDUE CFN A 6496
3	AC3	SOFTWARE	CYS A:62 , GLY A:87 , CYS A:88 , CYS A:154 , CYS B:70 , SER B:92 , CYS B:95 , TYR B:98 , THR B:152 , CYS B:153 , SER B:188	BINDING SITE FOR RESIDUE CLF B 6498
4	AC4	SOFTWARE	ASP B:353 , ASP B:357 , HOH B:835 , ARG D:108 , GLU D:109	BINDING SITE FOR RESIDUE CA B 524
5	AC5	SOFTWARE	ILE C:70 , ARG C:96 , HIS C:195 , TYR C:229 , CYS C:275 , GLY C:356 , GLY C:357 , ARG C:359 , PHE C:381 , HIS C:442 , HCA C:494	BINDING SITE FOR RESIDUE CFN C 7496
6	AC6	SOFTWARE	ALA C:65 , ARG C:96 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , HOH C:500 , HOH C:502 , HOH C:530 , HOH C:534 , HOH C:560 , HOH C:607 , HOH C:685 , HOH C:781 , CFN C:7496	BINDING SITE FOR RESIDUE HCA C 494
7	AC7	SOFTWARE	ARG B:108 , GLU B:109 , ASP D:353 , ASP D:357 , HOH D:599	BINDING SITE FOR RESIDUE CA D 524
8	AC8	SOFTWARE	CYS C:62 , GLY C:87 , CYS C:88 , CYS C:154 , CYS D:70 , SER D:92 , CYS D:95 , TYR D:98 , THR D:152 , CYS D:153 , SER D:188 , HOH D:619	BINDING SITE FOR RESIDUE CLF D 7498

(no "SS Bond" information available for 3K1A)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:253	-	Ser A:254
2	Gly A:448	-	Pro A:449
3	Tyr B:12	-	Pro B:13
4	Phe B:471	-	Pro B:472
5	Gly C:448	-	Pro C:449
6	Tyr D:12	-	Pro D:13
7	Phe D:471	-	Pro D:472

(no "SAP(SNP)/Variant" information available for 3K1A)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NITROGENASE_1_1	PS00699	Nitrogenases component 1 alpha and beta subunits signature 1.	NIFD_AZOVI	81-88	2	A:81-88 C:81-88
1	NITROGENASE_1_1	PS00699		NIFK_AZOVI	88-95	2	B:88-95 D:88-95
2	NITROGENASE_1_2	PS00090	Nitrogenases component 1 alpha and beta subunits signature 2.	NIFK_AZOVI	151-165	2	B:151-165 D:151-165
2	NITROGENASE_1_2	PS00090		NIFD_AZOVI	152-166	2	A:152-166 C:152-166

(no "Exon" information available for 3K1A)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:467
 aligned with NIFD_AZOVI | P07328 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:476
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474      
           NIFD_AZOVI     5 SREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE 480
               SCOP domains d3k1aa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3k1aA01 A:5-62,A:345-479                                  3k1aA02 A:63-205 Nitrogenase molybdenum iron protein domain                                                                                    3k1aA03 A:206-320 Nitrogenase molybdenum iron protein domain                                                       ------------------------3k1aA01 A:5-62,A:345-479 Nitrogenase molybdenum iron protein domain                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhhheee.---------.................hhhhhhh..........eeeee..hhhhhhh.....................ee...hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhh..hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh...............eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh..eeeehhhhhhhhhhh...eee..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------NITROGEN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1a A   5 SREEVESLIQEVLEVYPEKARKDRNKHLAVN---------CIISNKKSQPGLMTIRGCAYAGSKGIVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE 480
                                    14        24        34|        -|       54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474      
                                                         35        45

Chain B from PDB  Type:PROTEIN  Length:522
 aligned with NIFK_AZOVI | P07329 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:522
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521  
           NIFK_AZOVI     2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
               SCOP domains d3k1ab_ B: Nitrogenase iron-molybdenum protein, beta chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------3k1aB01 B:70-215 Nitrogenase molybdenum iron protein domain                                                                                       3k1aB02 B:216-320 Nitrogenase molybdenum iron protein domain                                             3k1aB03 B:321-364,B:485-523                 3k1aB04 B:365-470 Nitrogenase molybdenum iron protein domain                                              --------------3k1aB03 B:321-364,B:485-523             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh.hhhhh.......eeee.....hhhhhhhhhhhhhhhh..eee.....hhhhh.............hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh..eee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------NITROGEN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k1a B   2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

Chain C from PDB  Type:PROTEIN  Length:468
 aligned with NIFD_AZOVI | P07328 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:477
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       
           NIFD_AZOVI     5 SREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWEA 481
               SCOP domains d3k1ac_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3k1aC01 C:5-62,C:345-479                                  3k1aC02 C:63-205 Nitrogenase molybdenum iron protein domain                                                                                    3k1aC03 C:206-320 Nitrogenase molybdenum iron protein domain                                                       ------------------------3k1aC01 C:5-62,C:345-479 Nitrogenase molybdenum iron protein domain                                                                    -- CATH domains
           Pfam domains (1) ---------------------------------------------------------Oxidored_nitro-3k1aC01 C:62-468                                                                                                                                                                                                                                                                                                                                                                                        ------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------Oxidored_nitro-3k1aC02 C:62-468                                                                                                                                                                                                                                                                                                                                                                                        ------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhheee.---------.................hhhhhhh..........eeeee..hhhhhhh.....................ee...hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhh..hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh...............eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh..eeeehhhhhhhhhhh...eee..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------NITROGEN--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1a C   5 SREEVESLIQEVLEVYPEKARKDRNKHLAVN---------CIISNKKSQPGLMTIRGCAYAGSKGIVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWEA 481
                                    14        24        34|        -|       54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       
                                                         35        45

Chain D from PDB  Type:PROTEIN  Length:522
 aligned with NIFK_AZOVI | P07329 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:522
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521  
           NIFK_AZOVI     2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
               SCOP domains d3k1ad_ D: Nitrogenase iron-molybdenum protein, beta chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------3k1aD01 D:70-215 Nitrogenase molybdenum iron protein domain                                                                                       3k1aD02 D:216-320 Nitrogenase molybdenum iron protein domain                                             3k1aD03 D:321-364,D:485-523                 3k1aD04 D:365-470 Nitrogenase molybdenum iron protein domain                                              --------------3k1aD03 D:321-364,D:485-523             CATH domains
           Pfam domains (1) DUF3364-3k1aD01 D:2-56                                 -------------Oxidored_nitro-3k1aD03 D:70-502                                                                                                                                                                                                                                                                                                                                                                                                                  --------------------- Pfam domains (1)
           Pfam domains (2) DUF3364-3k1aD02 D:2-56                                 -------------Oxidored_nitro-3k1aD04 D:70-502                                                                                                                                                                                                                                                                                                                                                                                                                  --------------------- Pfam domains (2)
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh...eee.....hhhhh.............hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh..eee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------NITROGEN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k1a D   2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Chelatase-like (149)

Superfamily: Helical backbone metal receptor (102)

Family: Nitrogenase iron-molybdenum protein (41)

Protein domain: automated matches (6)

Azotobacter vinelandii [TaxId: 354] (6)

1a	d3k1aa_	A:
1b	d3k1ac_	C:

Protein domain: Nitrogenase iron-molybdenum protein, beta chain (20)

Azotobacter vinelandii [TaxId: 354] (15)

2a	d3k1ab_	B:
2b	d3k1ad_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)

Azotobacter vinelandii. Organism_taxid: 354. (1)

1a	3k1aA02	A:63-205
1b	3k1aC02	C:63-205
1c	3k1aA01	A:5-62,A:345-479
1d	3k1aC01	C:5-62,C:345-479
1e	3k1aB01	B:70-215
1f	3k1aD01	D:70-215
1g	3k1aA03	A:206-320
1h	3k1aC03	C:206-320
1i	3k1aB04	B:365-470
1j	3k1aD04	D:365-470
1k	3k1aB02	B:216-320
1l	3k1aD02	D:216-320

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 (19)

Homologous Superfamily: Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 (19)

Azotobacter vinelandii. Organism_taxid: 354. (1)

2a	3k1aB03	B:321-364,B:485-523
2b	3k1aD03	D:321-364,D:485-523

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DUF3364] (10)

Family: DUF3364 (10)

Azotobacter vinelandii (8)

1a	DUF3364-3k1aD01	D:2-56
1b	DUF3364-3k1aD02	D:2-56

Clan: no clan defined [family: Oxidored_nitro] (12)

Family: Oxidored_nitro (12)

Azotobacter vinelandii (8)

2a	Oxidored_nitro-3k1aC01	C:62-468
2b	Oxidored_nitro-3k1aC02	C:62-468
2c	Oxidored_nitro-3k1aD03	D:70-502
2d	Oxidored_nitro-3k1aD04	D:70-502

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (NIFD_AZOVI | P07328)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0018697	carbonyl sulfide nitrogenase activity	Catalysis of the reaction: carbonyl sulfide + 2 H+ + 2 e- = hydrogen sulfide + carbon monoxide.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016163	nitrogenase activity	Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0009399	nitrogen fixation	The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0016612	molybdenum-iron nitrogenase complex	An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.

Chain B,D (NIFK_AZOVI | P07329)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0018697	carbonyl sulfide nitrogenase activity	Catalysis of the reaction: carbonyl sulfide + 2 H+ + 2 e- = hydrogen sulfide + carbon monoxide.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016163	nitrogenase activity	Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0009399	nitrogen fixation	The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0016612	molybdenum-iron nitrogenase complex	An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.

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	3k1a
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(no "Related Entries Specified in the PDB File" available for 3K1A)

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

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