Structure of PDB 7ady Chain D

Receptor sequence

>7adyD (length=473) Species: 354 (Azotobacter vinelandii)

PMVLLECDKDIPERQKHIYLKAPNEDTREFLPIANAATIPGTLSERGCAF
CGAKLVIGGVLKDTIQMIHGPLGCAYDTWHTKRYPTDNGHFNMKYVWSTD
MKESHVVFGGEKRLEKSMHEAFDEMPDIKRMIVYTTCPTALIGDDIKAVA
KKVMKDRPDVDVFTVECPGFSGVSQSKGHHVLNIGWINEKVETMEKEITS
EYTMNFIGDFNIQGDTQLLQTYWDRLGIQVVAHFTGNGTYDDLRCMHQAQ
LNVVNCARSSGYIANELKKRYGIPRLDIDSWGFNYMAEGIRKICAFFGIE
EKGEELIAEEYAKWKPKLDWYKERLQGKKMAIWTGGPRLWHWTKSVEDDL
GVQVVAMSSKFGHEEDFEKVIARGKEGTYYIDDGNELEFFEIIDLVKPDV
IFTGPRVGELVKKLHIPYVNGHGYHNGPYMGFEGFVNLARDMYNAVHNPL
RHLAAVDIRDKSQTTPVIVRGAA

3D structure

• PDB: 7ady CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution.
• Chain: D
• Resolution: 1.05 Å

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.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	D6N	D	V57 K83 F211 C257 S260 G336 P338 R339 K361 F362 H423	V56 K82 F210 C256 S259 G335 P337 R338 K360 F361 H422
BS02	BCT	D	T335 G336 G337 P338 R339	T334 G335 G336 P337 R338
BS03	CLF	D	C49 F51 P72 G74 C75 T137 C138 G170	C48 F50 P71 G73 C74 T136 C137 G169

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)