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(-) Description

Title :  TVNIR IN COMPLEX WITH SULFITE, HIGH DOSE DATA SET
 
Authors :  V. A. Lazarenko, K. M. Polyakov, A. A. Trofimov, A. N. Popov, T. V. Tikhon A. V. Tikhonov, V. O. Popov
Date :  16 Apr 14  (Deposition) - 10 Sep 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  8 Hemes C, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Lazarenko, K. M. Polyakov, A. A. Trofimov, A. N. Popov, T. V. Tikhonova, A. V. Tikhonov, V. O. Popov
X-Ray-Induced Changes In The Active Site Structure Of Octaheme Cytochrome C Nitrite Reductase And Its Substrate Complexes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - EIGHT-HEME NITRITE REDUCTASE
    Chains: A, B
    Organism Scientific: THIOALKALIVIBRIO NITRATIREDUCENS
    Organism Taxid: 186931

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3HEC16Ligand/IonHEME C
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO35Ligand/IonSULFITE ION
Biological Unit 1 (4, 81)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3HEC48Ligand/IonHEME C
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO315Ligand/IonSULFITE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , VAL A:129 , ARG A:131 , ALA A:132 , ALA A:179 , CYS A:184 , CYS A:187 , LYS A:188 , ARG A:242 , CYS A:299 , HIS A:300 , TYR A:303 , CYS A:305 , HIS A:361 , ASN A:486 , HEC A:603 , SO3 A:609 , HOH A:702 , HOH A:719 , HOH A:824 , HOH A:982BINDING SITE FOR RESIDUE HEC A 601
02AC2SOFTWARECYS A:66 , HIS A:70 , GLN A:73 , LEU A:225 , CYS A:227 , CYS A:230 , HIS A:231 , ALA A:290 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HEC A:607 , HOH A:819 , HOH A:931 , HOH A:1013BINDING SITE FOR RESIDUE HEC A 602
03AC3SOFTWARESER A:84 , PRO A:116 , ARG A:117 , HIS A:119 , PHE A:121 , MET A:122 , ASP A:125 , CYS A:187 , LYS A:188 , LEU A:225 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , HEC A:601 , HEC A:604 , HOH A:704 , HOH A:709 , HOH A:739 , HOH A:875BINDING SITE FOR RESIDUE HEC A 603
04AC4SOFTWAREHIS A:300 , PHE A:367 , HIS A:372 , VAL A:377 , ALA A:378 , CYS A:379 , CYS A:382 , HIS A:383 , THR A:402 , PRO A:403 , ARG A:404 , LYS A:431 , ASN A:486 , PHE A:490 , HIS A:491 , HEC A:603 , HEC A:605 , HOH A:739 , HOH A:871 , HOH A:875 , HOH A:878 , HOH A:905 , HOH A:973BINDING SITE FOR RESIDUE HEC A 604
05AC5SOFTWAREASN A:141 , TRP A:142 , GLN A:143 , VAL A:371 , HIS A:372 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ILE A:427 , PHE A:490 , HEC A:604 , HOH A:880 , HOH A:1068 , HOH A:1098BINDING SITE FOR RESIDUE HEC A 605
06AC6SOFTWARECYS A:14 , PHE A:15 , HIS A:18 , ILE A:21 , HIS A:25 , VAL A:33 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , LEU A:194 , PHE A:228 , PRO A:233 , HIS A:234 , ARG A:239 , PHE A:274 , ARG A:276 , ARG A:282 , HEC A:607 , HEC A:608 , HOH A:788 , HOH A:969BINDING SITE FOR RESIDUE HEC A 606
07AC7SOFTWARELYS A:29 , HIS A:30 , HIS A:37 , ALA A:65 , CYS A:66 , THR A:68 , CYS A:69 , HIS A:70 , CYS A:227 , HIS A:231 , ALA A:236 , HEC A:602 , HEC A:606 , HOH A:1050 , HOH A:1155 , THR B:68 , HOH B:722BINDING SITE FOR RESIDUE HEC A 607
08AC8SOFTWAREGLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , VAL A:45 , ALA A:48 , SER A:49 , SER A:50 , ARG A:52 , MET A:53 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , HEC A:606 , HOH A:777 , HOH A:859 , HOH A:866 , HOH A:914 , HOH A:969 , HOH A:1053 , HOH A:1142BINDING SITE FOR RESIDUE HEC A 608
09AC9SOFTWAREPHE A:109 , ARG A:131 , TYR A:303 , GLN A:360 , HIS A:361 , HEC A:601 , HOH A:745 , HOH A:982 , HOH A:1076BINDING SITE FOR RESIDUE SO3 A 609
10BC1SOFTWAREGLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:748 , HOH A:800BINDING SITE FOR RESIDUE CA A 610
11BC2SOFTWARETHR A:68 , HOH A:767 , HOH A:1110 , HOH A:1166 , HIS B:70 , LYS B:393 , HEC B:602BINDING SITE FOR RESIDUE ACT A 611
12BC3SOFTWAREARG A:87 , GLN A:138 , PHE A:139 , TRP A:142 , ARG A:497 , HOH A:910BINDING SITE FOR RESIDUE MPD A 612
13BC4SOFTWAREHIS A:18 , THR A:19 , GLN A:20 , ILE A:21 , HOH A:969 , HOH A:1140BINDING SITE FOR RESIDUE SO3 A 613
14BC5SOFTWARETYR A:198 , LYS A:271 , THR A:273 , ARG A:282 , HOH A:834BINDING SITE FOR RESIDUE ACT A 614
15BC6SOFTWARESER A:50 , ARG A:51 , ARG B:252 , GLU B:341 , HOH B:819 , HOH B:965 , HOH B:1074BINDING SITE FOR RESIDUE SO3 A 615
16BC7SOFTWAREHIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , CYS B:184 , CYS B:187 , LYS B:188 , ARG B:242 , CYS B:299 , HIS B:300 , TYR B:303 , CYS B:305 , HIS B:361 , ASN B:486 , HEC B:603 , SO3 B:609 , HOH B:726 , HOH B:743 , HOH B:849 , HOH B:1008BINDING SITE FOR RESIDUE HEC B 601
17BC8SOFTWAREACT A:611 , CYS B:66 , HIS B:70 , GLN B:73 , LEU B:225 , CYS B:227 , CYS B:230 , HIS B:231 , MET B:384 , TYR B:395 , THR B:396 , HIS B:398 , HEC B:607 , HOH B:844 , HOH B:956 , HOH B:1039BINDING SITE FOR RESIDUE HEC B 602
18BC9SOFTWARESER B:84 , PRO B:116 , ARG B:117 , HIS B:119 , PHE B:121 , MET B:122 , ASP B:125 , CYS B:187 , LYS B:188 , LEU B:225 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , HEC B:601 , HEC B:604 , HOH B:728 , HOH B:733 , HOH B:763 , HOH B:900BINDING SITE FOR RESIDUE HEC B 603
19CC1SOFTWARECYS B:296 , HIS B:300 , PHE B:367 , HIS B:372 , ALA B:378 , CYS B:379 , CYS B:382 , HIS B:383 , THR B:402 , PRO B:403 , ARG B:404 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , HEC B:603 , HEC B:605 , HOH B:763 , HOH B:896 , HOH B:900 , HOH B:903 , HOH B:930 , HOH B:999BINDING SITE FOR RESIDUE HEC B 604
20CC2SOFTWAREASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , ASN B:375 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , HEC B:604 , HOH B:1095BINDING SITE FOR RESIDUE HEC B 605
21CC3SOFTWARECYS B:14 , PHE B:15 , HIS B:18 , ILE B:21 , HIS B:25 , VAL B:33 , ASN B:34 , CYS B:35 , CYS B:38 , HIS B:39 , THR B:59 , LEU B:194 , PHE B:228 , PRO B:233 , HIS B:234 , ARG B:239 , PHE B:274 , ARG B:276 , ARG B:282 , HEC B:607 , HEC B:608 , HOH B:812 , HOH B:995BINDING SITE FOR RESIDUE HEC B 606
22CC4SOFTWARETHR A:68 , HOH A:1166 , LYS B:29 , HIS B:30 , HIS B:37 , ALA B:65 , CYS B:66 , THR B:68 , CYS B:69 , HIS B:70 , CYS B:227 , HIS B:231 , ALA B:236 , HEC B:602 , HEC B:606 , HOH B:710 , HOH B:1077 , HOH B:1171BINDING SITE FOR RESIDUE HEC B 607
23CC5SOFTWAREGLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , HIS B:44 , VAL B:45 , ALA B:48 , SER B:49 , ARG B:51 , ARG B:52 , MET B:53 , ARG B:56 , PRO B:57 , THR B:59 , LEU B:194 , GLN B:275 , ARG B:276 , HEC B:606 , HOH B:801 , HOH B:884 , HOH B:891 , HOH B:939 , HOH B:995 , HOH B:1080 , HOH B:1184BINDING SITE FOR RESIDUE HEC B 608
24CC6SOFTWAREPHE B:109 , ARG B:131 , TYR B:303 , GLN B:360 , HIS B:361 , HEC B:601 , HOH B:769 , HOH B:1008 , HOH B:1103BINDING SITE FOR RESIDUE SO3 B 609
25CC7SOFTWAREGLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:772 , HOH B:824BINDING SITE FOR RESIDUE CA B 610
26CC8SOFTWAREHIS A:70 , LYS A:393 , THR B:68 , HOH B:722 , HOH B:724 , HOH B:791BINDING SITE FOR RESIDUE ACT B 611
27CC9SOFTWAREARG B:87 , GLN B:138 , PHE B:139 , TRP B:142 , ARG B:497 , HOH B:935BINDING SITE FOR RESIDUE MPD B 612
28DC1SOFTWAREHIS B:18 , THR B:19 , GLN B:20 , ILE B:21 , HOH B:908 , HOH B:995 , HOH B:1190BINDING SITE FOR RESIDUE SO3 B 613
29DC2SOFTWARETYR B:198 , LYS B:271 , HOH B:859BINDING SITE FOR RESIDUE ACT B 614

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q5B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q5B)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q5B)

(-) 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)
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:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.hhhhhhhhh.......hhhh.eehhhhhhhh.........ee...hhhhhh.hhhhhhhhhh...................hhhhhh..hhhhh......hhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.eee...................hhhhhhhh........hhhhh...........hhhhhhhh.....hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....ee...ee......ee...hhhhhee...hhhhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q5b A   5 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVA 523
                                    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       484       494       504       514         


Chain B from PDB  Type:PROTEIN  Length:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhh.hhhhhhhhh.......hhhh.eehhhhhhhh.........ee...hhhhhh.hhhhhhhhhh...................hhhhhhh.hhhhh......hhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.eee...................hhhhhh..........hhhhh...........hhhhhhhh.....hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....ee...ee......ee...hhhhhee...hhhhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q5b B   5 NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMGERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLIAGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRGAWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHEAAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGLGTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYNCNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGAALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPRDMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPVAKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSISKSKEAVSLLNDAIDAQVA 523
                                    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       484       494       504       514
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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)

(no "SCOP Domain" information available for 4Q5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q5B)

(-) Gene Ontology  (10, 10)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NIR_THIND | L0DSL2: 2ot4 2zo5 3d1i 3f29 3fo3 3gm6 3lg1 3lgq 3mmo 3owm 3rkh 3s7w 3sce 3uu9 4l38 4l3x 4l3y 4l3z 4q0t 4q17 4q1o 4q4u 4q5c

(-) Related Entries Specified in the PDB File

4q4u 4q5c