Structure of PDB 8bcx Chain D Binding Site BS04

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 504 [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)		R75 R110 G111 H112 M115 C136 V173 R190 V217 C218 C221 H222 V321
Binding residue
(residue number reindexed from 1)		R31 R66 G67 H68 M71 C92 V129 R146 V173 C174 C177 H178 V277
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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