Structure of PDB 3tor Chain D Binding Site BS03

Receptor Information
>3tor Chain D (length=441) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVEAKNETFAPQHPDQYLSWKATSEQSERVDALAEDPRLVILWAGYPFSR
DYNKPRGHAFAVTDVRETLRTGAPKNAEDGPLPMACWSCKSPDVARLIQK
DGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTLSRPYAA
RAMEAIGKPFEKAGRFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVE
NMEQYYDKIAFSDWTNSLSKTPMLKAQHPEYETWTAGIHGKNNVTCIDCH
MPKVQNAEGKLYTDHKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSI
NDLKIKVEDQLVHAHFEAKAALDAGATEAEMKPIQDDIRHAQWRWDLAIA
SHGIHMHAPEEGLRMLGTAMDKAADARTKLARLLATKGITHEIQIPDIST
KEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARKNGLLS
Ligand information
Ligand IDHEC
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
InChIKeyHXQIYSLZKNYNMH-LJNAALQVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
OpenEye OEToolkits 1.5.0CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
CACTVS 3.341C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
CACTVS 3.341CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
FormulaC34 H34 Fe N4 O4
NameHEME C
ChEMBL
DrugBank
ZINC
PDB chain3tor Chain D Residue 3 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3tor Characterization of the active site and calcium binding in cytochrome c nitrite reductases.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N89 P91 T104 R106 C122 C125 K126 C212 H213 Y216 F218 H264
Binding residue
(residue number reindexed from 1)		N53 P55 T68 R70 C86 C89 K90 C176 H177 Y180 F182 H228
Annotation score1
Enzymatic activity
Enzyme Commision number 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0005509 calcium ion binding
GO:0016491 oxidoreductase activity
GO:0016966 nitric oxide reductase activity
GO:0020037 heme binding
GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
GO:0046872 metal ion binding
Biological Process
GO:0009061 anaerobic respiration
GO:0019645 anaerobic electron transport chain
GO:0042128 nitrate assimilation
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3tor, PDBe:3tor, PDBj:3tor
PDBsum3tor
PubMed22103542
UniProtP0ABK9|NRFA_ECOLI Cytochrome c-552 (Gene Name=nrfA)

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