SMTL ID : 5bvh.1

CO-bound form of Selenium incorporated nitrogenase MoFe-protein (Av1-Se-CO) from A. vinelandii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 9 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.2, ICH.3 12 PLIP interactions: 10 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:E.380, A:E.380, A:K.426, A:K.426, B:Y.98, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.13: 9 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.14, ICH.15 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:G.95, C:K.426, C:K.426, C:K.426, C:Q.440, C:Q.440, 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: 16 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, ICH.3, CMO.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Salt bridges: A:E.380 Metal complexes: A:C.275, CMO.6, CMO.6 ICS.14: 16 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.13, ICH.15, CMO.18 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

2 x ICH: iron-sulfur-molybdenum cluster with interstitial carbon with selenium incorporated(Non-covalent)

ICH.3: 17 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, ICS.2, CMO.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Salt bridges: A:E.380 Metal complexes: A:C.275, CMO.6, CMO.6 ICH.15: 17 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.13, ICS.14, CMO.18 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

8 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 2 residues within 4Å: Chain A: E.287, W.294 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.294 pi-Stacking: A:W.294 IMD.8: 5 residues within 4Å: Chain B: L.253, D.256, G.275, T.276, E.280 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.256 Water bridges: B:L.253, 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:Y.233, B:S.482, B:Q.492 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 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.287 Water bridges: C:E.296 pi-Stacking: C:W.294 IMD.20: 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.21: 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.22: 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

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: R.93, T.104, T.111, M.112 Chain B: F.450, R.453 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain C: R.93, T.104, T.111, M.112 Chain D: F.450, R.453 Ligand excluded by PLIP

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

CMO.6: 6 residues within 4Å: Chain A: V.70, Q.191, H.195, F.381 Ligands: ICS.2, ICH.3 No protein-ligand interaction detected (PLIP) CMO.18: 6 residues within 4Å: Chain C: V.70, Q.191, H.195, F.381 Ligands: ICS.14, ICH.15 No protein-ligand interaction detected (PLIP)

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.19: 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)

FE2.11: 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.20, H2O.61 FE2.12: 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.26, H2O.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spatzal, T. et al., Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor. Elife (2015)

Release Date

2015-12-30

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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