Structure of PDB 4nd8 Chain D Binding Site BS02

Receptor Information
>4nd8 Chain D (length=522) Species: 354 (Azotobacter vinelandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKE
YQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRS
YFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVST
TCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMF
EGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGY
SLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKT
KKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRL
VDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKR
WKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFI
QRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSI
LERLDEETRGMQATDYNHDLVR
Ligand information
Ligand ID1CL
InChIInChI=1S/8Fe.7S
InChIKeyJKVMXLBGZBULKV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6[S]12[Fe][S]3[Fe]1[S]([Fe]2)[Fe]3S45[Fe]6[S]7[Fe]4[S]8[Fe]7[S]6[Fe]58
CACTVS 3.370[Fe]|1|2S|3[Fe]S|1[Fe]S|2[Fe]|3[S]45[Fe]|6S|7[Fe]|8S|6[Fe]4S|8[Fe]5|7
FormulaFe8 S7
NameFE(8)-S(7) CLUSTER, OXIDIZED
ChEMBL
DrugBank
ZINC
PDB chain4nd8 Chain C Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4nd8 Turnover-Dependent Inactivation of the Nitrogenase MoFe-Protein at High pH.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		C70 S92 G94 C95 Y98 C153 S188
Binding residue
(residue number reindexed from 1)		C69 S91 G93 C94 Y97 C152 S187
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) C153 V157
Catalytic site (residue number reindexed from 1) C152 V156
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4nd8, PDBe:4nd8, PDBj:4nd8
PDBsum4nd8
PubMed24392967
UniProtP07329|NIFK_AZOVI Nitrogenase molybdenum-iron protein beta chain (Gene Name=nifK)

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