SMTL ID : 8crs.1

CryoEM Structure of nitrogenase MoFe-protein in detergent

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.8: 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.9 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: 7 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Water bridges: A:R.97, A:K.426, A:K.426, A:K.426, A:K.426, A:E.440, A:E.440, A:E.440 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.9: 7 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.8 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:R.97, C:K.426, C:K.426, C:K.426, C:E.440, C:E.440, C:E.440 Salt bridges: C:K.426, C:H.442, C:H.442

4 x 1N7: CHAPSO(Non-covalent)

1N7.3: 8 residues within 4Å: Chain A: A.340, K.341, R.345, D.464 Chain D: H.362, E.388, P.413, Y.414 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:K.341, D:P.413, D:Y.414, D:Y.414 Hydrogen bonds: A:K.341, D:E.388 Water bridges: A:Y.342, A:Y.342 1N7.5: 7 residues within 4Å: Chain A: P.143, L.144 Chain B: Y.34, K.38, E.41, V.42, W.45 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:P.143, A:L.144, B:Y.34, B:K.38, B:E.41, B:V.42, B:W.45, B:W.45, B:W.45 1N7.6: 8 residues within 4Å: Chain B: H.362, E.388, P.413, Y.414 Chain C: A.340, K.341, R.345, D.464 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:P.413, B:Y.414, B:Y.414, C:K.341 Hydrogen bonds: B:E.388 Water bridges: C:Y.342, C:Y.342 1N7.12: 7 residues within 4Å: Chain C: P.143, L.144 Chain D: Y.34, K.38, E.41, V.42, W.45 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:P.143, C:L.144, D:Y.34, D:K.38, D:E.41, D:V.42, D:W.45, D:W.45, D:W.45

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

CLF.4: 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.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.69, B:C.94, B:C.94, B:C.152, A:C.62, A:C.88, A:C.88, A:C.154 Salt bridges: A:E.153 CLF.11: 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.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.69, D:C.94, D:C.94, D:C.152, 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.7: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.352, B:D.356, B:D.356, D:E.108, H2O.14 FE.10: 4 residues within 4Å: Chain B: R.107, E.108 Chain D: D.352, D.356 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.352, D:D.356, D:D.356, B:E.108, H2O.46

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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