Structure of PDB 5koj Chain D

Receptor sequence

>5kojD (length=510) Species: 272568 (Gluconacetobacter diazotrophicus PA1 5)

PQNVDKILDHAPLFREPEYQEMLAGKAKLENMPPADKVVEIADWTKSWEY
REKNFARESLSVNPAKACQPLGAVFVASGFERTMSFVHGSQGCVAYYRSH
LSRHFKEPSSAVSSSMTEDAAVFGGLNNMVDGLANTYKLYDPKMIAVSTT
CMAEVIGDDLHAFIQTAKGKGSVPEEFDVPFAHTPAFVGSHVTGYDNMLK
GILEHFWKGRTPVPNRSVNIIPGFDGFAVGNNRELKRILGMMGVQYTILS
DVSDQFDTPSDGEYRMYDGGTKIEAARDAVNADYTISLQEYCTPKTLEYC
QSFGQKTASFHYPLGIGATDDLLQKLSEISGKPVPQELEMERGRLVDALA
DSQAYLHGKTYAIYGDPDFVYGMARFILETGGEPKHCLATNGSKAWEAQM
QELFDSSPFGVGCKAWGGKDLWHMRSLLATEKVDLLIGNSYGKYLERDTD
TPLIRLMFPIFDRHHHHRFPVWGYQGALRVLVTLLDKIFDKLDDDTIQAG
VTDYSFDLTR

3D structure

• PDB: 5koj Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer.
• Chain: D
• Resolution: 2.592 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C152 V156
• Catalytic site (residue number reindexed from 1): C151 V155
• 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	FE	D	K107 E108	K106 E107
BS02	CLF	D	C69 G93 C94 Y97 Y98 T151 C152 A187	C68 G92 C93 Y96 Y97 T150 C151 A186
BS03	FE	D	D348 D352	D347 D351

Gene Ontology

Molecular Function

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

Biological Process

• GO:0009399 nitrogen fixation

Cellular Component

• GO:0016612 molybdenum-iron nitrogenase complex

External links

• PDB: RCSB:5koj, PDBe:5koj, PDBj:5koj
• PDBsum: 5koj
• PubMed: 27487256
• UniProt: A9H5W8