SMTL ID : 6o7s.1

Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the indigo carmine oxidized state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 11 residues within 4Å: Chain A: A.65, V.70, R.96, Q.191, G.424, I.425, K.426, H.442 Chain B: Y.98, R.105 Ligands: ICS.2 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Water bridges: A:G.95, A:R.96, A:R.96, A:K.426, A:K.426, A:K.426, A:E.440, B:Y.98, B:R.105, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.6: 11 residues within 4Å: Chain C: A.65, V.70, R.96, Q.191, G.424, I.425, K.426, H.442 Chain D: Y.98, R.105 Ligands: ICS.7 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:R.96, C:R.96, C:R.97, C:K.426, C:K.426, C:E.440, D:S.101, 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: 17 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, R.277, S.278, I.355, G.356, G.357, L.358, R.359, P.360, 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: 17 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, I.231, C.275, R.277, S.278, I.355, G.356, G.357, L.358, R.359, P.360, 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 NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: G.87, C.88 Ligands: LPJ.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.88 NA.8: 3 residues within 4Å: Chain C: G.87, C.88 Ligands: LPJ.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.88

2 x LPJ: FE(6)-S(7) CLUSTER(Non-covalent)

LPJ.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, A.188 Ligands: NA.3 7 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:C.70, B:C.95, B:C.153, A:C.62, A:C.88, A:C.154, LPJ.4 LPJ.9: 20 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, A.188 Ligands: NA.8 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: C:C.62, C:C.88, C:C.154, D:C.70, D:C.95, D:C.153, LPJ.9

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

FE.5: 5 residues within 4Å: Chain B: D.353, D.357 Chain C: K.433 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.41 FE.10: 5 residues within 4Å: Chain A: K.433 Chain B: R.108, E.109 Chain D: D.353, D.357 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.353, D:D.357, B:R.108, B:E.109, H2O.15, H2O.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rutledge, H.L. et al., Redox-Dependent Metastability of the Nitrogenase P-Cluster. J.Am.Chem.Soc. (2019)

Release Date

2019-06-19

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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