SMTL ID : 6cdk.1

Characterization of the P1+ intermediate state of nitrogenase P-cluster

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 6 residues within 4Å: Chain A: A.65, Q.191, G.424, I.425, H.442 Ligands: ICS.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.191, A:I.425 Water bridges: A:G.95, A:R.97, A:K.426, A:K.426, A:K.426, A:K.426, A:K.426, B:Y.98, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.6: 7 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.7 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:G.95, C:R.97, C:K.426, C:K.426, C:K.426, C:K.426, C:K.426, D:Y.98, D:Y.98, D:R.105 Salt bridges: C:K.426, C:H.442, C:H.442

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

ICS.2: 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.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICS.7: 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.6 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

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

CLF.3: 17 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, C.154, G.185 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 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.8: 16 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, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 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.4: 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.8, H2O.24 FE.5: 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.25, H2O.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keable, S.M. et al., Structural characterization of the P1+intermediate state of the P-cluster of nitrogenase. J. Biol. Chem. (2018)

Release Date

2018-05-09

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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