Structure of PDB 8w6x Chain S

Receptor sequence

>8w6xS (length=266) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F')

MGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAA
AGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRI
LPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCP
PNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGE
FAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIG
CSEPDFWDAMTPFYQN

3D structure

• PDB: 8w6x New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase.
• Chain: S
• Resolution: 1.04 Å

Enzymatic activity

• Enzyme Commision number: 1.12.2.1: cytochrome-c3 hydrogenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	SF4	S	E16 C17 G19 C20 G112 T113 C114 C150 P151	E15 C16 G18 C19 G111 T112 C113 C149 P150
BS02	SF4	S	H188 C191 R193 L194 C216 L217 Y218 C222	H187 C190 R192 L193 C215 L216 Y217 C221
BS03	F3S	S	N229 C231 F236 W241 P242 C249 I250 G251 C252	N228 C230 F235 W240 P241 C248 I249 G250 C251

Gene Ontology

Molecular Function

• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0047806 cytochrome-c3 hydrogenase activity
• GO:0051538 3 iron, 4 sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0009061 anaerobic respiration

Cellular Component

• GO:0016020 membrane
• GO:0042597 periplasmic space
• GO:0044569 [Ni-Fe] hydrogenase complex

External links

• PDB: RCSB:8w6x, PDBe:8w6x, PDBj:8w6x
• PDBsum: 8w6x
• PubMed: 37712026
• UniProt: P21853|PHNS_NITV9 Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)