SMTL ID : 8q5w.3 (5 other biounits)

MgADP-bound Fe protein of the molybdenum nitrogenase from Methanocaldococcus infernus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: R.108 Ligand excluded by PLIP

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

SF4.2: 12 residues within 4Å: Chain A: C.105, A.106, G.107, C.140, G.141, F.143 Chain B: C.105, A.106, G.107, C.140, G.141, F.143 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.105, B:C.140, A:C.105, A:C.140

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

ADP.3: 18 residues within 4Å: Chain A: K.18, G.20, I.21, G.22, K.23, S.24, T.25, N.193, I.219, P.220, R.221, D.222, V.225, Q.226, E.229, Q.244, Y.248 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.20, A:I.21, A:G.22, A:K.23, A:S.24, A:T.25, A:T.25, A:N.193, A:P.220, A:R.221, A:D.222, A:Q.226, A:E.229, A:Q.244 Salt bridges: A:K.23 pi-Cation interactions: A:R.195 ADP.5: 19 residues within 4Å: Chain B: K.18, G.20, I.21, G.22, K.23, S.24, T.25, N.193, I.219, P.220, R.221, D.222, V.225, Q.226, E.229, Q.244, Y.248 Ligands: MG.6, NO3.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.20, B:I.21, B:G.22, B:K.23, B:S.24, B:T.25, B:T.25, B:N.193, B:P.220, B:R.221, B:D.222, B:E.229, B:Q.244 Salt bridges: B:K.23

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: S.24, D.48, D.52, D.133 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.24, A:D.52 MG.6: 5 residues within 4Å: Chain B: S.24, D.48, D.52, S.53 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.24

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.7: 6 residues within 4Å: Chain B: S.24, Q.28, D.52, R.55, M.56 Ligands: ADP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.28, B:D.52, B:M.56 NO3.8: 2 residues within 4Å: Chain B: H.59, G.87 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maslac, N. et al., Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales. Febs J. (2024)

Release Date

2024-05-15

Peptides

Nitrogenase iron protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Nitrogenase iron protein

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