Structure of PDB 5xlf Chain L Binding Site BS03

Receptor Information
>5xlf Chain L (length=533) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRD
PRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQ
YLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKA
VQDKLKTFVESGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQ
VKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFV
DEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVV
FKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDR
YSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEA
LFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQA
EGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPVE
ASLIGTPVADAKRPVEILRTVHSFDPCIACGVH
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5xlf Chain L Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xlf Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		E62 L498 H552
Binding residue
(residue number reindexed from 1)		E43 L479 H533
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E34 C81 C84 H88 R479 S502 C546 C549
Catalytic site (residue number reindexed from 1) E15 C62 C65 H69 R460 S483 C527 C530
Enzyme Commision number 1.12.2.1: cytochrome-c3 hydrogenase.
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0016151 nickel cation binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0047806 cytochrome-c3 hydrogenase activity
Cellular Component
GO:0042597 periplasmic space

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Molecular Function
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Cellular Component
External links
PDB RCSB:5xlf, PDBe:5xlf, PDBj:5xlf
PDBsum5xlf
PubMed28967475
UniProtP21852|PHNL_NITV9 Periplasmic [NiFe] hydrogenase large subunit (Gene Name=hydB)

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