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(-) Description

Title :  TVNIR IN COMPLEX WITH SULFITE, LOW 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 :  15 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:833 , HOH A:1017 , HOH A:1188BINDING 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:295 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HEC A:603 , HEC A:607 , ACT A:617 , HOH A:827 , HOH A:954 , HOH A:1056BINDING 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:602 , HEC A:604 , HOH A:704 , HOH A:710 , HOH A:743 , HOH A:893BINDING 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:743 , HOH A:888 , HOH A:893 , HOH A:896 , HOH A:925 , HOH A:1004BINDING 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:874 , HOH A:1113 , HOH A:1153BINDING SITE FOR RESIDUE HEC A 605
06AC6SOFTWAREALA A:11 , CYS 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 , THR A:59 , ILE A:193 , 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:792 , HOH A:1000BINDING 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:617 , HOH A:1060 , HOH A:1112 , HOH A:1185 , HOH A:1227 , HOH A:1276 , 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 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , GLN A:275 , ARG A:276 , HEC A:606 , HOH A:782 , HOH A:876 , HOH A:883 , HOH A:936 , HOH A:1000 , HOH A:1121 , HOH A:1231 , HOH A:1252BINDING 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:783 , HOH A:1017 , HOH A:1188BINDING SITE FOR RESIDUE SO3 A 609
10BC1SOFTWAREGLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:752 , HOH A:807BINDING SITE FOR RESIDUE CA A 610
11BC2SOFTWARETHR A:68 , HOH A:771 , HOH A:1184 , HOH A:1189 , HOH A:1288 , HIS B:70 , HEC B:602 , HEC B:607 , HOH B:1295BINDING SITE FOR RESIDUE ACT A 611
12BC3SOFTWAREARG A:87 , GLN A:138 , PHE A:139 , TRP A:142 , ARG A:497 , HOH A:931BINDING SITE FOR RESIDUE MPD A 612
13BC4SOFTWAREHIS A:18 , THR A:19 , GLN A:20 , ILE A:21 , PHE A:274 , HOH A:901 , HOH A:1000 , HOH A:1247BINDING SITE FOR RESIDUE SO3 A 613
14BC5SOFTWARETYR A:198 , LYS A:271 , HOH A:843 , HOH A:1242BINDING SITE FOR RESIDUE ACT A 614
15BC6SOFTWAREMET A:99 , LYS A:102 , HOH A:894 , HOH A:932 , HOH A:1023BINDING SITE FOR RESIDUE TRS A 615
16BC7SOFTWARESER A:50 , ARG A:51 , ARG B:252 , LEU B:254 , GLU B:341 , HOH B:821 , HOH B:987 , HOH B:1288BINDING SITE FOR RESIDUE SO3 A 616
17BC8SOFTWAREHIS A:70 , HEC A:602 , HEC A:607 , HOH A:1185 , HOH A:1287 , HOH A:1289 , THR B:68BINDING SITE FOR RESIDUE ACT A 617
18BC9SOFTWAREHIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , ALA B:179 , 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:724 , HOH B:742 , HOH B:855 , HOH B:1039 , HOH B:1209BINDING SITE FOR RESIDUE HEC B 601
19CC1SOFTWAREACT A:611 , CYS B:66 , HIS B:70 , GLN B:73 , LEU B:225 , CYS B:227 , CYS B:230 , HIS B:231 , ALA B:290 , MET B:384 , TYR B:395 , THR B:396 , HIS B:398 , HEC B:603 , HEC B:607 , HOH B:849 , HOH B:977 , HOH B:1078BINDING SITE FOR RESIDUE HEC B 602
20CC2SOFTWARESER 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:602 , HEC B:604 , HOH B:726 , HOH B:732 , HOH B:764 , HOH B:915BINDING SITE FOR RESIDUE HEC B 603
21CC3SOFTWAREARG B:96 , 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:764 , HOH B:910 , HOH B:915 , HOH B:918 , HOH B:948 , HOH B:1026BINDING SITE FOR RESIDUE HEC B 604
22CC4SOFTWAREASN 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:896 , HOH B:938 , HOH B:1135 , HOH B:1175BINDING SITE FOR RESIDUE HEC B 605
23CC5SOFTWARECYS 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 , 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:813 , HOH B:1022BINDING SITE FOR RESIDUE HEC B 606
24CC6SOFTWARETHR A:68 , ACT A:611 , HOH A:1288 , 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:1082 , HOH B:1134 , HOH B:1254 , HOH B:1269 , HOH B:1295BINDING SITE FOR RESIDUE HEC B 607
25CC7SOFTWAREGLN 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:898 , HOH B:905 , HOH B:959 , HOH B:1022 , HOH B:1143 , HOH B:1283BINDING SITE FOR RESIDUE HEC B 608
26CC8SOFTWAREPHE B:109 , ARG B:131 , TYR B:303 , GLN B:360 , HIS B:361 , HEC B:601 , HOH B:804 , HOH B:1039 , HOH B:1209BINDING SITE FOR RESIDUE SO3 B 609
27CC9SOFTWAREGLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:773 , HOH B:828BINDING SITE FOR RESIDUE CA B 610
28DC1SOFTWAREARG B:87 , GLN B:138 , PHE B:139 , TRP B:142 , ARG B:497 , HOH B:954BINDING SITE FOR RESIDUE MPD B 611
29DC2SOFTWAREHIS B:18 , THR B:19 , GLN B:20 , ILE B:21 , PHE B:274 , HOH B:923 , HOH B:1022BINDING SITE FOR RESIDUE SO3 B 612
30DC3SOFTWARETYR B:198 , LYS B:271 , HOH B:865BINDING SITE FOR RESIDUE ACT B 613
31DC4SOFTWAREMET B:99 , LYS B:102 , HOH B:916 , HOH B:931 , HOH B:955 , HOH B:1045BINDING SITE FOR RESIDUE TRS B 614

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q4U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q4U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q4U)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q4U)

(-) 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.hhhhhhhhhhhhhhhhhheee...................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
                 4q4u 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
                 4q4u 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 4Q4U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q4U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q4U)

(-) Gene Ontology  (10, 10)

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    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4q5b 4q5c

(-) Related Entries Specified in the PDB File

4q5b 4q5c