Structure of PDB 5bvh Chain C Binding Site BS02

Receptor Information
>5bvh Chain C (length=477) Species: 354 (Azotobacter vinelandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQ
PGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGT
TGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSE
CPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVR
DWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQW
SGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPT
KTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVML
YIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDD
VTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFRQMHSWDYSGPYHGF
DGFAIFARDMDMTLNNPCWKKLQAPWE
Ligand information
Ligand IDICH
InChIInChI=1S/C.7Fe.Mo.6S.3Se
InChIKeyWTYUMBSEMHMDAI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C12345[Fe]67[S]8[Fe]19[S]1[Fe]8[S]6[Fe]21[Se][Fe]31[S]2[Fe]4([Se]7)[S]3[Fe]5([S]1[Mo]32)[Se]9
CACTVS 3.385S1[Fe]S[Fe@@]23S[Fe]4[Se][Fe]5S[Fe@@]67S[Mo]S[Fe]([Se]2)[C]3456[Fe]1[Se]7
CACTVS 3.385S1[Fe]S[Fe]23S[Fe]4[Se][Fe]5S[Fe]67S[Mo]S[Fe]([Se]2)[C]3456[Fe]1[Se]7
FormulaC Fe7 Mo S6 Se3
Nameiron-sulfur-molybdenum cluster with interstitial carbon with selenium incorporated
ChEMBL
DrugBank
ZINC
PDB chain5bvh Chain C Residue 503 [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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PDB5bvh Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor.
Resolution1.53 Å
Binding residue
(original residue number in PDB)		V70 R96 H195 Y229 I231 C275 S278 I355 G356 G357 L358 R359 F381 H442
Binding residue
(residue number reindexed from 1)		V67 R93 H192 Y226 I228 C272 S275 I352 G353 G354 L355 R356 F378 H439
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C62 A65 R96 H195
Catalytic site (residue number reindexed from 1) C59 A62 R93 H192
Enzyme Commision number 1.18.6.1: nitrogenase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016163 nitrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
Biological Process
GO:0009399 nitrogen fixation
Cellular Component
GO:0016612 molybdenum-iron nitrogenase complex

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5bvh, PDBe:5bvh, PDBj:5bvh
PDBsum5bvh
PubMed26673079
UniProtP07328|NIFD_AZOVI Nitrogenase molybdenum-iron protein alpha chain (Gene Name=nifD)

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