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(-) Description

Title :  TVNIR IN COMPLEX WITH SULFITE, MIDDLE 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) - 03 Sep 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
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  (6, 31)

Asymmetric Unit (6, 31)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3HEC16Ligand/IonHEME C
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO35Ligand/IonSULFITE ION
6TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (5, 87)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3HEC48Ligand/IonHEME C
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5SO315Ligand/IonSULFITE ION
6TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , VAL A:129 , ARG A:131 , 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:720 , HOH A:830 , HOH A:1013BINDING 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:603 , HEC A:607 , ACT A:616 , HOH A:824 , HOH A:951 , HOH A:1052BINDING 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 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , HEC A:601 , HEC A:602 , HEC A:604 , HOH A:704 , HOH A:710 , HOH A:741 , HOH A:890BINDING SITE FOR RESIDUE HEC A 603
04AC4SOFTWAREHIS A:300 , PHE A:367 , HIS A:372 , 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:741 , HOH A:885 , HOH A:890 , HOH A:893 , HOH A:922 , HOH A:1001BINDING 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 , HEC A:604 , HOH A:871 , HOH A:895 , HOH A:913 , HOH A:1111 , HOH A:1149BINDING 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:791 , HOH A:997BINDING 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 , ACT A:616 , HOH A:1110 , HOH A:1177 , HOH A:1224 , HOH A:1269 , THR B:68BINDING 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 , GLN A:275 , ARG A:276 , HEC A:606 , HOH A:780 , HOH A:873 , HOH A:880 , HOH A:933 , HOH A:997 , HOH A:1119 , HOH A:1228 , HOH A:1249BINDING 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:781 , HOH A:1013BINDING SITE FOR RESIDUE SO3 A 609
10BC1SOFTWAREGLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:750 , HOH A:805BINDING SITE FOR RESIDUE CA A 610
11BC2SOFTWAREARG A:87 , GLN A:138 , PHE A:139 , TRP A:142 , ARG A:497 , HOH A:928BINDING SITE FOR RESIDUE MPD A 611
12BC3SOFTWAREHIS A:18 , THR A:19 , GLN A:20 , ILE A:21 , PHE A:274 , HOH A:997 , HOH A:1244BINDING SITE FOR RESIDUE SO3 A 612
13BC4SOFTWARETYR A:198 , LYS A:271 , HOH A:841 , HOH A:1239BINDING SITE FOR RESIDUE ACT A 613
14BC5SOFTWAREMET A:99 , LYS A:102 , HOH A:891 , HOH A:929 , HOH A:1019BINDING SITE FOR RESIDUE TRS A 614
15BC6SOFTWARESER A:50 , ARG A:51 , ARG B:252 , LEU B:254 , GLU B:341 , HOH B:822 , HOH B:986 , HOH B:1291BINDING SITE FOR RESIDUE SO3 A 615
16BC7SOFTWAREHIS A:70 , HEC A:602 , HEC A:607 , HOH A:1177 , HOH A:1279 , THR B:68 , HOH B:792BINDING SITE FOR RESIDUE ACT A 616
17BC8SOFTWAREHIS 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:610 , HOH B:725 , HOH B:743 , HOH B:854 , HOH B:1038BINDING SITE FOR RESIDUE HEC B 601
18BC9SOFTWARECYS 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:603 , HEC B:607 , ACT B:609 , HOH B:848 , HOH B:976 , HOH B:1077BINDING SITE FOR RESIDUE HEC B 602
19CC1SOFTWARESER 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 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , HEC B:601 , HEC B:602 , HEC B:604 , HOH B:727 , HOH B:733 , HOH B:764 , HOH B:914BINDING SITE FOR RESIDUE HEC B 603
20CC2SOFTWAREHIS B:300 , PHE B:367 , HIS B:372 , ALA B:378 , CYS B:379 , CYS B:382 , HIS B:383 , THR B:402 , ARG B:404 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , HEC B:603 , HEC B:605 , HOH B:764 , HOH B:909 , HOH B:914 , HOH B:917 , HOH B:947 , HOH B:1026BINDING SITE FOR RESIDUE HEC B 604
21CC3SOFTWAREASN 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:895 , HOH B:937 , HOH B:1135 , HOH B:1173BINDING SITE FOR RESIDUE HEC B 605
22CC4SOFTWARECYS 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 , ILE B:193 , 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:814 , HOH B:1022BINDING SITE FOR RESIDUE HEC B 606
23CC5SOFTWARETHR A:68 , 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 , ACT B:609 , HOH B:710 , HOH B:1134 , HOH B:1201 , HOH B:1257 , HOH B:1272BINDING SITE FOR RESIDUE HEC B 607
24CC6SOFTWAREGLN 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:803 , HOH B:897 , HOH B:904 , HOH B:958 , HOH B:1022 , HOH B:1143 , HOH B:1286BINDING SITE FOR RESIDUE HEC B 608
25CC7SOFTWARETHR A:68 , HIS B:70 , HEC B:602 , HEC B:607 , HOH B:720 , HOH B:722 , HOH B:1201BINDING SITE FOR RESIDUE ACT B 609
26CC8SOFTWAREPHE B:109 , ARG B:131 , TYR B:303 , GLN B:360 , HIS B:361 , HEC B:601 , HOH B:804 , HOH B:1038BINDING SITE FOR RESIDUE SO3 B 610
27CC9SOFTWAREGLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:773 , HOH B:828BINDING SITE FOR RESIDUE CA B 611
28DC1SOFTWAREARG B:87 , GLN B:138 , PHE B:139 , TRP B:142 , ARG B:497 , HOH B:953BINDING SITE FOR RESIDUE MPD B 612
29DC2SOFTWAREHIS B:18 , THR B:19 , GLN B:20 , ILE B:21 , PHE B:274 , HOH B:922 , HOH B:1022BINDING SITE FOR RESIDUE SO3 B 613
30DC3SOFTWARETYR B:198 , LYS B:271 , HOH B:865BINDING SITE FOR RESIDUE ACT B 614
31DC4SOFTWARELYS B:102 , HOH B:915 , HOH B:930 , HOH B:954 , HOH B:1044BINDING SITE FOR RESIDUE TRS B 615

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q5C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q5C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q5C)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q5C)

(-) 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...................hhhhhhh.hhhhhh.....hhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.eee...................hhhhhhhh........hhhhh...........hhhhhhhh.....hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....eee..ee......ee...hhh.eee......hhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q5c 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.hhhhhh.....hhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhheee...................hhhhhhhh........hhhhh...........hhhhhhhh.....hhhhh........ee.hhhhhhhhh.........hhhhhhhh.eeeeeeee..eeeeeeeee...hhhhhhh.....eee..ee......ee...hhh.eee...hhhhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.................hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q5c 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 4Q5C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q5C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q5C)

(-) Gene Ontology  (10, 10)

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(-) 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 4q5b

(-) Related Entries Specified in the PDB File

4q4u 4q5b