SMTL ID : 9cje.1

CryoEM structure of nitrogenase MoFe-protein 20 second time point under alkaline turnover

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

ICS.1: 15 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.2 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICS.5: 9 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, M.441, H.442 1 PLIP interactions: 1 interactions with chain C, Metal complexes: C:C.275

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

HCA.2: 9 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Chain B: S.101 Ligands: ICS.1 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425, B:Y.98, B:Y.98, B:S.101 Water bridges: A:G.95, A:K.426, A:K.426, A:K.426, A:E.440, A:E.440, A:S.443, A:S.443, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442

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

CLF.3: 19 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 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: 4 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.70, B:C.95, B:C.95, B:C.153, A:C.62, A:C.88, A:C.88, A:C.154 Salt bridges: A:E.153 CLF.7: 19 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain D: 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 C, 4 interactions with chain D, Salt bridges: C:E.153 Metal complexes: C:C.62, C:C.88, C:C.88, C:C.154, D:C.70, D:C.95, D:C.95, D:C.153

2 x FE: FE (III) ION(Non-covalent)

FE.4: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:R.108, D:E.109, B:D.353, H2O.19, H2O.20 FE.6: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:R.108, B:E.109, D:D.353, H2O.10, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warmack, R.A. et al., Structural evolution of nitrogenase states under alkaline turnover. Nat Commun (2024)

Release Date

2024-12-18

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

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