Structure of PDB 6z8j Chain D Binding Site BS01

Receptor Information

>6z8j Chain D (length=481) Species: 882 (Nitratidesulfovibrio vulgaris str. Hildenborough)

GRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDP
RDASQIVQRICGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANY
LQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIE
ALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVR
DFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMP
GVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYS
FVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLG
EEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEG
TGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEA
LIGIPVDDIQNPVNVARLIRAFDPCLGCAVH

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: 6z8j Chain C Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6z8j Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
• Resolution: 1.09 Å
• Binding residue (original residue number in PDB): R73 H185
• Binding residue (residue number reindexed from 1): R59 H171
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): E28 C75 C78 H82 R422 S445 C489 C492
• Catalytic site (residue number reindexed from 1): E14 C61 C64 H68 R408 S431 C475 C478
• Enzyme Commision number: 1.12.7.2: ferredoxin hydrogenase.

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008901 ferredoxin hydrogenase activity
• GO:0016151 nickel cation binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:6z8j, PDBe:6z8j, PDBj:6z8j
• PDBsum: 6z8j
• PubMed: 32865640
• UniProt: Q72AS3