SMTL ID : 8q50.1

Nitrogenase Fe protein from Methanothermococcus thermolithotrophicus, tetragonal crystalline form at 1.91-A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: D.9 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.9, H2O.3, H2O.4 CA.8: 1 residues within 4Å: Chain B: D.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, H2O.7, H2O.9

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 8 residues within 4Å: Chain A: C.105, A.106, G.107, C.140, G.142, F.143 Chain B: C.105 Ligands: FES.9 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.105, A:C.140 FES.9: 8 residues within 4Å: Chain A: C.105 Chain B: C.105, A.106, G.107, C.140, G.142, F.143 Ligands: FES.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.105, B:C.140

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: E.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.260 Water bridges: A:E.260, A:E.260 GOL.7: 7 residues within 4Å: Chain A: G.22, T.25, P.220, R.221, D.222, V.225, Q.226 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.22, A:P.220, A:D.222, A:Q.226, A:Q.226 Water bridges: A:T.26 GOL.10: 1 residues within 4Å: Chain B: E.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.260 Water bridges: B:E.260, B:E.260 GOL.14: 7 residues within 4Å: Chain B: G.22, T.25, P.220, R.221, D.222, V.225, Q.226 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.22, B:P.220, B:D.222, B:Q.226, B:Q.226 Water bridges: B:Y.248

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain A: L.177, P.264, T.265, P.266 No protein-ligand interaction detected (PLIP) ACT.5: 4 residues within 4Å: Chain A: I.6, R.118, D.149, L.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.149 Salt bridges: A:R.118 ACT.6: 5 residues within 4Å: Chain A: G.19, G.20, G.22, K.23, S.24 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.20, A:G.22, A:K.23, A:S.24 Water bridges: A:I.21, A:T.25, A:K.50 Salt bridges: A:K.23 ACT.11: 4 residues within 4Å: Chain B: L.177, P.264, T.265, P.266 No protein-ligand interaction detected (PLIP) ACT.12: 4 residues within 4Å: Chain B: I.6, R.118, D.149, L.151 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.149, B:D.149 Salt bridges: B:R.118 ACT.13: 5 residues within 4Å: Chain B: G.19, G.20, G.22, K.23, S.24 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.20, B:G.22, B:K.23, B:S.24 Water bridges: B:I.21, B:T.25, B:K.50 Salt bridges: B:K.23

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 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nitrogenase iron protein 1

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