SMTL ID : 6bbl.1

Crystal structure of the a-96Gln MoFe protein variant in the presence of the substrate acetylene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

hetero-2-2-mer

Ligands

2 x C2H: acetylene(Non-covalent)

C2H.1: 8 residues within 4Å: Chain A: A.65, G.66, G.69, V.70, Q.96, Q.191 Ligands: HCA.3, ICS.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.70, A:Q.191 C2H.9: 9 residues within 4Å: Chain C: A.65, G.66, G.69, V.70, Q.96, Q.191 Chain D: Y.98 Ligands: HCA.10, ICS.11 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.65, C:V.70

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 3 residues within 4Å: Chain A: E.287, W.294, M.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.294 Water bridges: A:W.294 pi-Stacking: A:W.294, A:W.294 IMD.12: 2 residues within 4Å: Chain C: R.343, E.368 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.343 Water bridges: C:R.343 pi-Cation interactions: C:R.343 IMD.14: 6 residues within 4Å: Chain C: G.157, L.158, F.186, R.187 Chain D: E.120, A.123 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.157, D:E.120

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

HCA.3: 11 residues within 4Å: Chain A: A.65, Q.96, Q.191, G.424, I.425, K.426, H.442 Chain B: Y.98, R.105 Ligands: C2H.1, ICS.4 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Water bridges: A:K.426, A:K.426, A:K.426, A:K.426, A:E.440, A:S.443, B:Y.98, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.10: 11 residues within 4Å: Chain C: A.65, Q.96, Q.191, G.424, I.425, K.426, H.442 Chain D: Y.98, R.105 Ligands: C2H.9, ICS.11 18 PLIP interactions: 2 interactions with chain D, 16 interactions with chain C Water bridges: D:Y.98, D:R.105, C:G.95, C:K.426, C:K.426, C:K.426, C:K.426, C:E.440, C:E.440, C:S.443, C:S.443 Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.96, C:Q.191, C:I.425 Salt bridges: C:K.426, C:H.442, C:H.442

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

ICS.4: 19 residues within 4Å: Chain A: V.70, Q.96, Q.191, 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: C2H.1, HCA.3 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICS.11: 19 residues within 4Å: Chain C: V.70, Q.96, Q.191, 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: C2H.9, HCA.10 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

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

1CL.5: 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.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 11 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A, 1 Ligand-Ligand interactions 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, 1CL.5 Salt bridges: A:E.153 1CL.13: 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.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 11 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D, 1 Ligand-Ligand interactions 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, D:S.188, 1CL.13

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

FE.6: 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 B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.353, B:D.357, D:R.108, D:E.109, H2O.20, H2O.73 FE.8: 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.28, H2O.64

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain B: W.361, K.365, I.501, L.505 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keable, S.M. et al., Structural characterization of the nitrogenase molybdenum-iron protein with the substrate acetylene trapped near the active site. J. Inorg. Biochem. (2017)

Release Date

2018-01-10

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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