SMTL ID : 6y1x.1 (1 other biounit)

X-ray structure of the radical SAM protein NifB, a key nitrogenase maturating enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 13 residues within 4Å: Chain A: H.37, C.39, F.40, R.50, H.52, E.75, V.106, A.108, A.110, C.138, S.140, T.162, K.215 7 PLIP interactions: 7 interactions with chain A, Salt bridges: A:E.75, A:E.75, A:E.75 Metal complexes: A:C.39, A:H.52, A:E.75, A:C.138 SF4.2: 11 residues within 4Å: Chain A: C.59, I.61, Q.62, C.63, Y.65, C.66, R.68, C.72, V.73, N.74, N.142 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.59, A:C.63, A:C.66, A:C.72

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: I.181, Y.182, K.183, G.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.184 Water bridges: A:K.183 SO4.4: 2 residues within 4Å: Chain A: K.64, K.254 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.64, A:K.254

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: L.31, R.32, R.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fajardo, A.S. et al., Structural Insights into the Mechanism of the Radical SAM Carbide Synthase NifB, a Key Nitrogenase Cofactor Maturating Enzyme. J.Am.Chem.Soc. (2020)

Release Date

2020-06-17

Peptides

Radical SAM domain protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Radical SAM domain protein

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