Structure of PDB 6qii Chain A Binding Site BS01

Receptor Information

>6qii Chain A (length=437) Species: 1434108 (Methanosarcina barkeri MS)

TKVVEISPTTRLEGHSKLTLKVNDQGIVERGDWLSITPVRGIEKLAIGKT
MEQVPKIASRVCGICPIAHTLASTEAMEASIGCEIPTDAKLLRIILHAAN
RIHSHALHNILILPDFYIPGTEKKFNLFANEQPARSVMARIVRIREIAQT
IAAIAGGEAIHPSNPRIGGMYHNVSPRAKQKMADLAKECLVLVHEQMEFM
LDVIRNMQNREFVEVGGKQIPLPKKLGYHNQGVMATAPMYGSSSLDDNPT
WDFTRWKETRPWDWYMGEVTIDLEDPSYPIGGTTKVGTKANPQMESCTGV
PTYDGQPVEVGPRARLATFKNFDEKGTFAQHIARQMEYPDCCYTILNCLD
NLNTSGKVLADHIPQGDGSMGWAANEAPRGSNIHLARVKDGKVRWYDMLV
PTTWNFPTCSRALTGAPWQIAEMVVRAYDPCVSCATH

Ligand information

• Ligand ID: SF4
• InChI: InChI=1S/4Fe.4S
• InChIKey: LJBDFODJNLIPKO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
  CACTVS 3.385: S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
• Formula: Fe4 S4
• Name: IRON/SULFUR CLUSTER
• PDB chain: 6qii Chain G Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qii X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases.
• Resolution: 2.28 Å
• Binding residue (original residue number in PDB): R61 H162
• Binding residue (residue number reindexed from 1): R60 H161
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): R380 T403 C432 C435
• Catalytic site (residue number reindexed from 1): R379 T402 C431 C434
• Enzyme Commision number: 1.12.98.1: coenzyme F420 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:0050454 coenzyme F420 hydrogenase activity
• GO:0050660 flavin adenine dinucleotide binding
• GO:0051536 iron-sulfur cluster binding

External links

• PDB: RCSB:6qii, PDBe:6qii, PDBj:6qii
• PDBsum: 6qii
• PubMed: 31591784
• UniProt: A0A0E3QYL7