SMTL ID : 9hb9.1

A. vinelandii nitrogenase MoFe protein Anc1a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.1: 16 residues within 4Å: Chain A: V.80, R.106, H.205, Y.239, I.241, C.285, S.288, V.365, G.366, G.367, L.368, R.369, F.391, M.451, H.452 Ligands: HCA.2 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.390 Metal complexes: A:C.285 ICS.5: 16 residues within 4Å: Chain C: V.80, R.106, H.205, Y.239, I.241, C.285, S.288, V.365, G.366, G.367, L.368, R.369, F.391, M.451, H.452 Ligands: HCA.6 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.390 Metal complexes: C:C.285

2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.2: 6 residues within 4Å: Chain A: A.75, Q.201, G.434, I.435, H.452 Ligands: ICS.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.201, A:I.435 Water bridges: A:K.436 Salt bridges: A:K.436, A:H.452, A:H.452 HCA.6: 7 residues within 4Å: Chain C: A.75, Q.201, G.434, I.435, K.436, H.452 Ligands: ICS.5 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.201, C:I.435, D:Y.98, D:Y.98 Salt bridges: C:K.436, C:H.452, C:H.452

2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.3: 19 residues within 4Å: Chain A: C.72, Y.74, P.95, G.97, C.98, Y.101, E.163, C.164, G.195 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.163 Metal complexes: A:C.72, A:C.98, A:C.98, A:C.164, B:C.70, B:C.95, B:C.95, B:C.153 CLF.7: 17 residues within 4Å: Chain C: C.72, Y.74, P.95, C.98, Y.101, E.163, C.164, G.195 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D, Salt bridges: C:E.163 Metal complexes: C:C.72, C:C.98, C:C.98, C:C.164, D:C.70, D:C.95, D:C.95, D:C.153

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain B: D.353, D.357 Chain D: F.107, R.108, E.109 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:R.108, D:E.109, B:D.353, B:D.357, H2O.2 MG.8: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.353, D:D.357, B:R.108, B:E.109, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuevas-Zuviria, B. et al., Structural evolution of nitrogenase enzymes over geologic time. Elife (2025)

Release Date

2025-09-10

Peptides

MoFe nitrogenase subunit D: AC
Nitrogenase molybdenum-iron protein beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

MoFe nitrogenase subunit D

Nitrogenase molybdenum-iron protein beta chain

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