SMTL ID : 9hbc.1

A. vinelandii nitrogenase MoFe protein Anc2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 8 residues within 4Å: Chain A: A.75, R.106, Q.201, G.433, I.434, K.435, H.451 Ligands: ICS.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.451 Hydrogen bonds: A:Q.201, A:I.434 Water bridges: A:G.105, A:R.107, A:K.435, A:K.435, A:K.435, A:K.435, A:K.435, B:R.105 Salt bridges: A:K.435, A:H.451, A:H.451 HCA.7: 8 residues within 4Å: Chain C: A.75, R.106, Q.201, G.433, I.434, K.435, H.451 Ligands: ICS.8 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.451 Hydrogen bonds: C:Q.201, C:I.434 Water bridges: C:G.105, C:K.435, C:K.435, C:K.435, C:K.435, D:R.105 Salt bridges: C:K.435, C:H.451, C:H.451

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

ICS.2: 15 residues within 4Å: Chain A: V.80, R.106, H.205, Y.238, I.240, C.284, S.287, V.364, G.365, G.366, L.367, R.368, F.390, H.451 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.389 Metal complexes: A:C.284 ICS.8: 15 residues within 4Å: Chain C: V.80, R.106, H.205, Y.238, I.240, C.284, S.287, V.364, G.365, G.366, L.367, R.368, F.390, H.451 Ligands: HCA.7 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.389 Metal complexes: C:C.284

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

CLF.3: 18 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, 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.9: 18 residues within 4Å: Chain C: C.72, Y.74, P.95, G.97, 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: 4 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.70, D:C.95, D:C.95, D:C.153, C:C.72, C:C.98, C:C.98, C:C.164 Salt bridges: C:E.163

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain A: T.111, W.245 Chain B: F.15, K.21, L.24 Chain D: A.514, Y.517 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Water bridges: D:Q.513, D:A.514 Hydrogen bonds: A:T.111

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain B: R.59, E.60, A.61, L.62, G.424, H.429 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:K.140, B:R.59, B:G.424, B:K.425 Hydrogen bonds: B:E.60 EDO.10: 4 residues within 4Å: Chain D: L.466, I.467, R.468, R.476 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.466, D:R.468, D:R.468, D:R.476, D:R.476

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:R.108, D:E.109, B:D.353, B:D.357, H2O.12, H2O.40 MG.11: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:R.108, B:E.109, D:D.353, D:D.357, H2O.17, H2O.35

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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