SMTL ID : 8dbx.1

CryoEM structure of partially oxidized MoFe-protein on ultrathin carbon

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.6: 15 residues within 4Å: Chain C: 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.7 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

2 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, E.440, H.442 Ligands: ICS.1 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Water bridges: B:S.101, A:K.426 Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.7: 8 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:A.65, C:K.426, C:K.426 Salt bridges: C:K.426, C:H.442, C:H.442

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

CLF.3: 20 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 Ligands: 1CL.4 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.70, B:C.95, B:C.95, B:C.153, B:S.188, A:C.62, A:C.88, A:C.88, A:C.154 Salt bridges: A:E.153 CLF.9: 19 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, 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 Ligands: 1CL.10 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 1CL: FE(8)-S(7) CLUSTER, OXIDIZED(Covalent)(Non-covalent)

1CL.4: 20 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 Ligands: CLF.3 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.70, B:C.95, B:C.95, B:C.153, B:S.188, A:C.62, A:C.88, A:C.88, A:C.154 Salt bridges: A:E.153 1CL.10: 19 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, 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 Ligands: CLF.9 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.70, D:C.95, D:C.95, D:C.153, D:S.188, C:C.62, C:C.88, C:C.88, C:C.154 Salt bridges: C:E.153

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

FE.5: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:E.109, B:D.353, B:D.353, B:D.357, H2O.8 FE.8: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.353, D:D.353, D:D.357, B:E.109, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warmack, R.A. et al., Structural consequences of turnover-induced homocitrate loss in nitrogenase. Nat Commun (2023)

Release Date

2023-03-08

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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