SMTL ID : 7qqa.2 (1 other biounit)

MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: K.9, G.11, I.12, G.13, K.14, S.15, T.16, N.184, V.210, P.211, R.212, D.213, V.216, Q.217, E.220, Q.235 Ligands: MG.2 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:K.9, A:G.11, A:I.12, A:G.13, A:K.14, A:S.15, A:T.16, A:T.16, A:N.184, A:P.211, A:R.212, A:D.213, A:Q.217, A:E.220, A:Q.235 Water bridges: A:K.14, A:S.15, A:S.15, A:S.15, A:S.15, A:S.15, A:S.15, A:S.15, A:D.39, A:K.41, A:R.212, A:E.220 Salt bridges: A:K.14 pi-Cation interactions: A:R.212, A:R.212 ADP.4: 17 residues within 4Å: Chain B: K.9, G.11, I.12, G.13, K.14, S.15, T.16, N.184, V.210, P.211, R.212, D.213, V.216, Q.217, E.220, Q.235 Ligands: MG.5 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.11, B:I.12, B:G.13, B:K.14, B:S.15, B:T.16, B:T.16, B:N.184, B:P.211, B:R.212, B:D.213, B:Q.217, B:E.220, B:Q.235 Water bridges: B:S.15, B:S.15, B:Q.19, B:D.39, B:K.41, B:R.46, B:R.212 Salt bridges: B:K.14 pi-Cation interactions: B:R.212, B:R.212

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.15, D.43 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.15, H2O.1, H2O.2, H2O.3, H2O.4 MG.5: 4 residues within 4Å: Chain B: S.15, D.39, D.43 Ligands: ADP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.15, H2O.10, H2O.11, H2O.11, H2O.11

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

SF4.3: 12 residues within 4Å: Chain A: C.96, A.97, G.98, C.131, G.133, F.134 Chain B: C.96, A.97, G.98, C.131, G.132, F.134 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.96, A:C.131, B:C.96, B:C.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trncik, C. et al., MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii. Journal of Inorganic Biochemistry (2022)

Release Date

2022-06-22

Peptides

Nitrogenase iron protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Nitrogenase iron protein

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