4ZK8 - JenaLib

Title :   COPPER-CONTAINING NITRITE REDUCTASE FROM THERMOPHILIC BACTERIUM GEOBACILLUS THERMODENITRIFICANS (RE-REFINED)

Authors :   Y. Fukuda, T. Inoue

Date :   30 Apr 15 (Deposition) - 20 May 15 (Release) - 20 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Copper, Oxidoreductase, Denitrification, Electron Transfer, Nitrite (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Fukuda, K. M. Tse, M. Lintuluoto, Y. Fukunishi, E. Mizohata, H. Matsumura, H. Takami, M. Nojiri, T. Inoue
Structural Insights Into The Function Of A Thermostable Copper-Containing Nitrite Reductase
J. Biochem. V. 155 123 2014
PubMed-ID: 24293549 | Reference-DOI: 10.1093/JB/MVT107

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 29)

Asymmetric Unit (8, 29)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CL	2	Ligand/Ion	CHLORIDE ION
3	CU	18	Ligand/Ion	COPPER (II) ION
4	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
5	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
6	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
7	SO4	1	Ligand/Ion	SULFATE ION
8	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (6, 27)

No.	Name	Count	Type	Full Name
1	ACY	6	Ligand/Ion	ACETIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	CU	-1	Ligand/Ion	COPPER (II) ION
4	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
5	MPD	9	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
6	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
7	SO4	3	Ligand/Ion	SULFATE ION
8	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Sites (29, 29)

Asymmetric Unit (29, 29)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:95 , CYS A:135 , HIS A:143 , MET A:148	binding site for residue CU A 401
02	AC2	SOFTWARE	HIS A:100 , HIS A:134 , HIS A:294 , CL A:419 , HOH A:507	binding site for residue CU A 402
03	AC3	SOFTWARE	HIS A:42 , GLU A:53 , HIS A:83 , HOH A:567 , HOH A:750	binding site for residue CU A 403
04	AC4	SOFTWARE	GLU A:226 , HOH A:646 , HOH A:720 , HOH A:760	binding site for residue CU A 404
05	AC5	SOFTWARE	GLU A:169 , MPD A:421 , ACY A:427 , HOH A:520 , HOH A:732	binding site for residue CU A 405
06	AC6	SOFTWARE	ASP A:40 , GLU A:217 , CU A:417 , HOH A:515 , HOH A:637 , HOH A:757	binding site for residue CU A 406
07	AC7	SOFTWARE	ASP A:251 , CU A:408 , HOH A:508 , HOH A:516	binding site for residue CU A 407
08	AC8	SOFTWARE	ASP A:251 , CU A:407 , HOH A:508 , HOH A:516 , HOH A:535	binding site for residue CU A 408
09	AC9	SOFTWARE	ASP A:55 , HOH A:510 , HOH A:523 , HOH A:526 , HOH A:673 , HOH A:786	binding site for residue CU A 409
10	AD1	SOFTWARE	HIS A:39 , HOH A:719 , HOH A:769	binding site for residue CU A 410
11	AD2	SOFTWARE	GLU A:165 , ASP A:167 , HOH A:511 , HOH A:541 , HOH A:627 , HOH A:653 , HOH A:801	binding site for residue CU A 411
12	AD3	SOFTWARE	LYS A:127 , ASP A:251 , THR A:282	binding site for residue CU A 412
13	AD4	SOFTWARE	PRO A:191 , GLU A:239 , ASN A:297 , HIS A:298 , CU A:418 , HOH A:501 , HOH A:549 , HOH A:663 , HOH A:739 , HOH A:815	binding site for residue CU A 413
14	AD5	SOFTWARE	ASP A:182 , HOH A:662 , HOH A:701 , HOH A:770	binding site for residue CU A 414
15	AD6	SOFTWARE	HIS A:262 , HOH A:797	binding site for residue CU A 415
16	AD7	SOFTWARE	GLU A:78 , HOH A:504 , HOH A:583 , HOH A:736 , HOH A:746	binding site for residue CU A 416
17	AD8	SOFTWARE	GLU A:217 , CU A:406 , HOH A:515 , HOH A:637 , HOH A:757	binding site for residue CU A 417
18	AD9	SOFTWARE	GLU A:239 , CU A:413 , HOH A:501 , HOH A:549 , HOH A:560 , HOH A:658 , HOH A:739 , HOH A:815 , HOH A:853	binding site for residue CU A 418
19	AE1	SOFTWARE	HIS A:134 , HIS A:244 , VAL A:246 , HIS A:294 , CU A:402 , HOH A:507 , HOH A:802	binding site for residue CL A 419
20	AE2	SOFTWARE	LYS A:157	binding site for residue CL A 420
21	AE3	SOFTWARE	ASP A:167 , ARG A:168 , GLU A:169 , CU A:405 , HOH A:520 , HOH A:528	binding site for residue MPD A 421
22	AE4	SOFTWARE	ARG A:285 , HOH A:566 , HOH A:585 , HOH A:846 , HOH A:875	binding site for residue MPD A 422
23	AE5	SOFTWARE	LYS A:22 , GLY A:23 , ASP A:51 , LYS A:61 , HOH A:665 , HOH A:731	binding site for residue MPD A 423
24	AE6	SOFTWARE	LYS A:32 , MET A:33 , GLU A:34 , HIS A:42 , GLU A:44 , HOH A:578 , HOH A:796	binding site for residue PEG A 424
25	AE7	SOFTWARE	LYS A:216 , PRO A:219 , MET A:306 , HOH A:867	binding site for residue EDO A 425
26	AE8	SOFTWARE	HIS A:262 , LEU A:263	binding site for residue SO4 A 426
27	AE9	SOFTWARE	GLU A:169 , LEU A:201 , TYR A:231 , CU A:405 , HOH A:520 , HOH A:732	binding site for residue ACY A 427
28	AF1	SOFTWARE	ARG A:168	binding site for residue ACY A 428
29	AF2	SOFTWARE	SER A:107 , GLY A:287 , THR A:288 , LYS A:308 , HOH A:527	binding site for residue TRS A 429

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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)
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Chain A from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.........eeeeee..eeeeeeeeeeeeeeee..eeeeeeee........eeee..eeeeeeeee.........ee.....hhhhhh.......eeeeeeee...eeeeee....hhhhhhhh..eeeeeee......hhhhh.eeeeeeeeee....hhhhhhhh...eeeeee..............hhhhhh.eeee...eeeeeeeeee....eeeee....eeeeee......eeeee..eee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zk8 A  18 IAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTE 311
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:69 - Pro A:70	[ RasMol ]
		Gly A:236 - Pro A:237	[ RasMol ]
		Lys A:138 - Pro A:139	[ RasMol ]

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		Biological Unit 1	[ Jena3D ]

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