Structure of PDB 8bcx Chain D Binding Site BS05

Receptor Information
>8bcx Chain D (length=444) Species: 269799 (Geobacter metallireducens GS-15) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTVQIPDGEVDPAVWGKAYPTEYEMWKKTKRGFDADHVTYDKLSEFPYMA
LLFNGWGFGIAYNEPRGHANMVRDQLEIDSARLKSGGVCLTCKTPYAPKL
EKEMGIDYFKTPFKDVLAKIPEKHKTLGVACIDCHDNKDMSLRISRGFTL
GEALKKLGVDQAKLSRQEMRSLVCAQCHVTYNIPKDADKKSIGVYFPWQG
SKMGNISVENIIKQIRSDASVGEWTQTVTGFKLGFIRHPEYELFSNNSVH
WKAGAACTDCHMPYTRVGAFKVSDHRVMSPLKNDMKACIQCHTEKPEWLR
DQVIAIQDRTVSLMLRSGYATATVAKLFEKAHAAQAQGKQIDKALYDRAK
DLYEEAFYRCVFIGAENSVGFHNPTEAMRVLGDATAFATKAEALLRQALA
KAGVDVPLTVNLELNKYLDQRGEKKLTFDPKVEIKDPYGVQVRF
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 chain8bcx Chain D Residue 505 [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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PDB8bcx An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens.
Resolution1.941 Å
Binding residue
(original residue number in PDB)		D80 Y106 E108 R110 L120 C133 C136 K137 C221 H222 Y225 H282 E284
Binding residue
(residue number reindexed from 1)		D36 Y62 E64 R66 L76 C89 C92 K93 C177 H178 Y181 H238 E240
Annotation score1
Enzymatic activity
Enzyme Commision number 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).
Gene Ontology
Molecular Function
GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:8bcx, PDBe:8bcx, PDBj:8bcx
PDBsum8bcx
PubMed37460131
UniProtQ39YY5

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