SMTL ID : 4tkv.1

CO-bound Nitrogenase MoFe-protein from A. vinelandii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 8 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICE.2 11 PLIP interactions: 10 interactions with chain A, 1 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, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.14: 8 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICE.15 15 PLIP interactions: 2 interactions with chain D, 13 interactions with chain C Water bridges: D:Y.98, D:R.105, C:G.95, C:R.97, C:K.426, C:K.426, C:K.426, C:Q.440, C:Q.440 Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Salt bridges: C:K.426, C:H.442, C:H.442

4 x ICE: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICE.2: 15 residues within 4Å: Chain A: V.70, R.96, 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, CMO.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Salt bridges: A:E.380 Metal complexes: A:C.275, CMO.4, CMO.4 ICE.6: 6 residues within 4Å: Chain A: R.93, T.104, T.111, M.112 Chain B: F.450, R.453 No protein-ligand interaction detected (PLIP) ICE.15: 15 residues within 4Å: Chain C: V.70, R.96, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.14, CMO.17 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275 ICE.19: 6 residues within 4Å: Chain C: R.93, T.104, T.111, M.112 Chain D: F.450, R.453 No protein-ligand interaction detected (PLIP)

8 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 1 residues within 4Å: Chain A: W.294 4 PLIP interactions: 4 interactions with chain A Water bridges: A:W.294, A:E.296, A:E.296 pi-Stacking: A:W.294 IMD.8: 5 residues within 4Å: Chain B: L.253, D.256, G.275, T.276, E.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.256 Water bridges: B:E.258, B:G.275 IMD.9: 7 residues within 4Å: Chain B: I.469, S.482, T.483, T.484, Q.492, I.493, T.496 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.482, B:Q.492 Water bridges: B:Y.233 IMD.10: 5 residues within 4Å: Chain A: G.157, L.158, F.186 Chain B: E.120, A.123 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.187 IMD.16: 2 residues within 4Å: Chain C: E.287, W.294 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.287 Water bridges: C:E.287, C:W.294, C:E.296 pi-Stacking: C:W.294, C:W.294 IMD.21: 7 residues within 4Å: Chain D: I.469, S.482, T.483, T.484, Q.492, I.493, T.496 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.483, D:T.496 Water bridges: D:S.482 IMD.22: 5 residues within 4Å: Chain D: L.253, D.256, G.275, T.276, E.280 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.256, D:E.280 Water bridges: D:L.253, D:E.258 IMD.23: 5 residues within 4Å: Chain C: G.157, L.158, F.186 Chain D: E.120, A.123 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.187

6 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.4: 5 residues within 4Å: Chain A: V.70, Q.191, H.195, F.381 Ligands: ICE.2 No protein-ligand interaction detected (PLIP) CMO.5: 5 residues within 4Å: Chain A: Y.100, T.104, T.111 Chain B: F.450, R.453 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.453, A:T.111 CMO.11: 3 residues within 4Å: Chain B: L.466, I.467, R.468 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Water bridges: D:E.503 Hydrogen bonds: B:R.468, B:R.468 CMO.17: 5 residues within 4Å: Chain C: V.70, Q.191, H.195, F.381 Ligands: ICE.15 No protein-ligand interaction detected (PLIP) CMO.18: 5 residues within 4Å: Chain C: Y.100, T.104, T.111 Chain D: F.450, R.453 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.453 CMO.24: 3 residues within 4Å: Chain D: L.466, I.467, R.468 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.468, D:R.468

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

CLF.7: 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 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.153 Metal complexes: A:C.62, A:C.88, A:C.88, A:C.154, B:C.70, B:C.95, B:C.95, B:C.153 CLF.20: 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 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D, 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

2 x FE2: FE (II) ION(Non-covalent)

FE2.12: 4 residues within 4Å: Chain B: D.353, D.357 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.18, H2O.56 FE2.13: 4 residues within 4Å: 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.25, H2O.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spatzal, T. et al., Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase. Science (2014)

Release Date

2014-10-01

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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