Structure of PDB 6z8j Chain D Binding Site BS04

Receptor Information
>6z8j Chain D (length=481) Species: 882 (Nitratidesulfovibrio vulgaris str. Hildenborough) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDP
RDASQIVQRICGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANY
LQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIE
ALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVR
DFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMP
GVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYS
FVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLG
EEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEG
TGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEA
LIGIPVDDIQNPVNVARLIRAFDPCLGCAVH
Ligand information
Ligand IDNI
InChIInChI=1S/Ni/q+2
InChIKeyVEQPNABPJHWNSG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ni++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ni+2]
FormulaNi
NameNICKEL (II) ION
ChEMBL
DrugBankDB14204
ZINC
PDB chain6z8j Chain D Residue 502 [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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PDB6z8j Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
Resolution1.09 Å
Binding residue
(original residue number in PDB)		A75 C78 U489 C492
Binding residue
(residue number reindexed from 1)		A61 C64 U475 C478
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E28 C75 C78 H82 R422 S445 C489 C492
Catalytic site (residue number reindexed from 1) E14 C61 C64 H68 R408 S431 C475 C478
Enzyme Commision number 1.12.7.2: ferredoxin hydrogenase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008901 ferredoxin hydrogenase activity
GO:0016151 nickel cation binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:6z8j, PDBe:6z8j, PDBj:6z8j
PDBsum6z8j
PubMed32865640
UniProtQ72AS3

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