SMTL ID : 8bts.2 (1 other biounit)

Nitrogenase MoFe protein from A. vinelandii alpha double mutant C45A/L158C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 10 residues within 4Å: Chain A: A.73, G.103, R.104, Q.199, G.432, I.433, K.434, H.450 Chain B: Y.98 Ligands: ICS.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.450 Hydrogen bonds: A:Q.199, A:I.433, B:Y.98 Salt bridges: A:K.434, A:H.450 HCA.7: 8 residues within 4Å: Chain C: A.73, R.104, Q.199, G.432, I.433, Q.448, H.450 Ligands: ICS.8 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:H.450 Hydrogen bonds: C:Q.199, C:I.433, C:H.450 Salt bridges: C:K.434, C:H.450, C:H.450

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

ICS.2: 15 residues within 4Å: Chain A: V.78, R.104, H.203, Y.237, I.239, C.283, S.286, I.363, G.364, G.365, L.366, R.367, F.389, H.450 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.388 Metal complexes: A:C.283 ICS.8: 15 residues within 4Å: Chain C: V.78, R.104, H.203, Y.237, I.239, C.283, S.286, I.363, G.364, G.365, L.366, R.367, F.389, H.450 Ligands: HCA.7 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.388 Metal complexes: C:C.283

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: K.349, R.353 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.349, A:R.353 SO4.5: 3 residues within 4Å: Chain B: N.399, K.400, R.401 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.400, B:R.401 Salt bridges: B:R.401 SO4.10: 3 residues within 4Å: Chain B: K.417 Chain C: K.349, R.353 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:K.349, C:R.353, B:K.417 SO4.13: 3 residues within 4Å: Chain D: N.399, K.400, R.401 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.400, D:R.401 SO4.14: 1 residues within 4Å: Chain D: R.206 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.206

2 x 1CL: FE(8)-S(7) CLUSTER, OXIDIZED(Non-covalent)

1CL.4: 19 residues within 4Å: Chain A: C.70, Y.72, P.93, G.95, C.96, Y.99, E.161, C.162, G.193 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Salt bridges: A:E.161 Metal complexes: A:C.70, A:C.96, A:C.96, A:C.162, B:C.70, B:C.95, B:C.95, B:C.153, B:S.188 1CL.11: 18 residues within 4Å: Chain C: C.70, Y.72, P.93, G.95, C.96, Y.99, E.161, C.162, G.193 Chain D: 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 C, 5 interactions with chain D, Salt bridges: C:E.161 Metal complexes: C:C.70, C:C.96, C:C.96, C:C.162, D:C.70, D:C.95, D:C.95, D:C.153, D:S.188

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

FE.6: 5 residues within 4Å: Chain B: D.353, D.357 Chain C: F.437 Chain D: R.108, E.109 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Metal complexes: B:D.353, B:D.357, B:D.357, D:R.108 FE.15: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Metal complexes: B:R.108, B:E.109, D:D.353, D:D.353, D:D.357

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain C: H.204, D.208, R.211, Y.289 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.208, C:R.211 GOL.12: 1 residues within 4Å: Chain D: E.42 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.42, D:E.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cadoux, C. et al., Nitrogen Fixation and Hydrogen Evolution by Sterically Encumbered Mo-Nitrogenase. Jacs Au (2023)

Release Date

2023-06-07

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
J

B
I

D
L

Nitrogenase protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

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