Structure of PDB 8bj7 Chain A Binding Site BS01

Receptor Information

>8bj7 Chain A (length=395) Species: 876 (Desulfovibrio desulfuricans)

SRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIF
GEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVK
CIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADV
TIWEEGSEFVERLTKKSDMPLPQFTSACPGWQKYAETYYPELLPHFSTCK
SPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGM
RDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGG
VMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVH
GAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLE

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: 8bj7 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bj7 Binding of exogenous cyanide reveals new active-site states in [FeFe] hydrogenases.
• Resolution: 1.04 Å
• Binding residue (original residue number in PDB): C179 C234 M376 A377 C378 C382
• Binding residue (residue number reindexed from 1): C178 C233 M375 A376 C377 C381
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.12.7.2: ferredoxin hydrogenase.

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0008901 ferredoxin hydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:8bj7, PDBe:8bj7, PDBj:8bj7
• PDBsum: 8bj7
• PubMed: 36937599
• UniProt: P07598|PHFL_NITV2 Periplasmic [Fe] hydrogenase large subunit (Gene Name=hydA)