Structure of PDB 7ady Chain D Binding Site BS02

Receptor Information

>7ady Chain D (length=473) Species: 354 (Azotobacter vinelandii)

PMVLLECDKDIPERQKHIYLKAPNEDTREFLPIANAATIPGTLSERGCAF
CGAKLVIGGVLKDTIQMIHGPLGCAYDTWHTKRYPTDNGHFNMKYVWSTD
MKESHVVFGGEKRLEKSMHEAFDEMPDIKRMIVYTTCPTALIGDDIKAVA
KKVMKDRPDVDVFTVECPGFSGVSQSKGHHVLNIGWINEKVETMEKEITS
EYTMNFIGDFNIQGDTQLLQTYWDRLGIQVVAHFTGNGTYDDLRCMHQAQ
LNVVNCARSSGYIANELKKRYGIPRLDIDSWGFNYMAEGIRKICAFFGIE
EKGEELIAEEYAKWKPKLDWYKERLQGKKMAIWTGGPRLWHWTKSVEDDL
GVQVVAMSSKFGHEEDFEKVIARGKEGTYYIDDGNELEFFEIIDLVKPDV
IFTGPRVGELVKKLHIPYVNGHGYHNGPYMGFEGFVNLARDMYNAVHNPL
RHLAAVDIRDKSQTTPVIVRGAA

Ligand information

• Ligand ID: BCT
• InChI: InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1
• InChIKey: BVKZGUZCCUSVTD-UHFFFAOYSA-M
• SMILES:
  OpenEye OEToolkits 1.5.0: C(=O)(O)[O-]
  CACTVS 3.341: OC([O-])=O
  ACDLabs 10.04: [O-]C(=O)O
• Formula: C H O3
• Name: BICARBONATE ION
• PDB chain: 7ady Chain D Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ady CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution.
• Resolution: 1.05 Å
• Binding residue (original residue number in PDB): T335 G336 G337 P338 R339
• Binding residue (residue number reindexed from 1): T334 G335 G336 P337 R338
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C49 C52 K83 H180
• Catalytic site (residue number reindexed from 1): C48 C51 K82 H179
• Enzyme Commision number: 1.18.6.1: nitrogenase.

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016163 nitrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051212 vanadium ion binding
• GO:0051536 iron-sulfur cluster binding

Biological Process

• GO:0009399 nitrogen fixation

External links

• PDB: RCSB:7ady, PDBe:7ady, PDBj:7ady
• PDBsum: 7ady
• PubMed: 32915491
• UniProt: P16855|VNFD_AZOVI Nitrogenase vanadium-iron protein alpha chain (Gene Name=vnfD)