Structure of PDB 6z8o Chain A Binding Site BS04

Receptor Information

>6z8o Chain A (length=277) Species: 882 (Nitratidesulfovibrio vulgaris str. Hildenborough)

RPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEH
AIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALK
EFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNI
PGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRN
IHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGV
NWCVQNAVCIGCVEPDFPDGKSPFYQA

Ligand information

• Ligand ID: 6ML
• InChI: InChI=1S/4Fe.2O.H2S.3S/h;;;;;;1H2;;;/q;;;+1;;;;;;/p-1
• InChIKey: DCVJTSMMUVGUAG-UHFFFAOYSA-M
• SMILES:
  OpenEye OEToolkits 2.0.5: O1[Fe](O[Fe]2S[Fe]3[S]2[Fe]1S3)[S]
  CACTVS 3.385: S.O1[Fe]O[Fe]2S[Fe](S[Fe]1)S2
• Formula: Fe4 O2 S4
• Name: oxygen-damaged SF4
• PDB chain: 6z8o Chain A Residue 304

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6z8o Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): C18 G20 C21 E77 G119 C121 C159 P160
• Binding residue (residue number reindexed from 1): C12 G14 C15 E71 G113 C115 C153 P154
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C18 C21 C121 C159 H208 C211 C232 C238 C247 C259 C265 C268
• Catalytic site (residue number reindexed from 1): C12 C15 C115 C153 H202 C205 C226 C232 C241 C253 C259 C262
• Enzyme Commision number: 1.12.2.1: cytochrome-c3 hydrogenase.

Gene Ontology

Molecular Function

• GO:0008901 ferredoxin hydrogenase activity
• GO:0051536 iron-sulfur cluster binding

Cellular Component

• GO:0009375 ferredoxin hydrogenase complex

External links

• PDB: RCSB:6z8o, PDBe:6z8o, PDBj:6z8o
• PDBsum: 6z8o
• PubMed: 32865640
• UniProt: Q72AS4