SMTL ID : 7szf.1

Structure of the Rieske Non-heme Iron Oxygenase GxtA with beta-Saxitoxinol Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-trimer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: H.30, L.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.30 GOL.2: 5 residues within 4Å: Chain A: P.47, I.48, C.109, Q.110, E.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.48, A:E.111 Water bridges: A:I.48 GOL.4: 5 residues within 4Å: Chain A: W.12, Y.107, H.108, C.109, Q.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.108, A:C.109, A:Q.110 Water bridges: A:Y.107 GOL.5: 2 residues within 4Å: Chain A: R.291, T.330 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.291 Water bridges: A:T.3, A:E.248, A:R.291, A:T.330 GOL.6: 3 residues within 4Å: Chain A: K.17, E.19, D.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.19, A:D.20 Water bridges: A:K.17, A:K.17 GOL.14: 4 residues within 4Å: Chain B: Y.138, H.139, K.140, K.263 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.138, B:K.140, B:K.140, B:K.263 GOL.15: 3 residues within 4Å: Chain B: E.248, R.291, T.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.291, B:T.330 Water bridges: B:R.291 GOL.16: 4 residues within 4Å: Chain B: T.194, G.196, W.217, R.219 No protein-ligand interaction detected (PLIP) GOL.18: 4 residues within 4Å: Chain B: W.12, H.108, C.109, Q.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.108, B:C.109, B:Q.110 GOL.22: 3 residues within 4Å: Chain C: H.139, K.140, K.263 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.139, C:K.140, C:K.140 GOL.23: 4 residues within 4Å: Chain C: P.47, I.48, C.109, E.111 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.48, C:I.48, C:E.111, C:E.111 GOL.25: 4 residues within 4Å: Chain C: T.28, A.29, H.30, I.246 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.28, C:T.28 Water bridges: C:H.30, C:H.30 GOL.26: 4 residues within 4Å: Chain C: Q.288, P.289, T.290, R.291 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.288, C:Q.288, C:T.290, C:T.290, C:R.291 GOL.27: 4 residues within 4Å: Chain C: T.194, K.197, W.217, R.219 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.219, C:R.219

3 x D82: beta-Saxitoxinol(Non-covalent)

D82.3: 12 residues within 4Å: Chain A: S.159, F.165, N.216, Q.226, C.228, D.239, M.241, Y.255, D.272, Y.273, V.276, D.280 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.226, A:Q.226, A:D.280 Water bridges: A:N.216, A:N.216, A:Q.226, A:T.230, A:T.230, A:Y.255, A:Y.273 Salt bridges: A:D.239 D82.17: 11 residues within 4Å: Chain B: S.159, F.165, N.216, Q.226, C.228, D.239, M.241, Y.255, D.272, Y.273, V.276 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.226, B:Q.226, B:Y.273, B:Y.273, B:D.280 Water bridges: B:N.216, B:N.216, B:N.216, B:Q.226, B:Q.226, B:D.239, B:D.272, B:Y.273 Salt bridges: B:D.239 D82.24: 12 residues within 4Å: Chain C: S.159, F.165, I.172, N.216, Q.226, C.228, D.239, M.241, Y.255, D.272, Y.273, V.276 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Q.226, C:Q.226, C:Y.255, C:D.280 Water bridges: C:N.216, C:N.216, C:Q.226, C:T.230, C:T.230, C:Y.273 Salt bridges: C:D.239

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

FE.7: 3 residues within 4Å: Chain A: H.164, H.169, D.280 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.164, A:H.169, A:D.280, H2O.6, H2O.6 FE.19: 4 residues within 4Å: Chain B: N.158, H.164, H.169, D.280 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.164, B:H.169, B:D.280, H2O.16, H2O.17 FE.28: 3 residues within 4Å: Chain C: H.164, H.169, D.280 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.164, C:H.169, C:D.280, H2O.29, H2O.29

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.8: 8 residues within 4Å: Chain A: C.55, H.57, R.58, C.74, Y.76, H.77, G.78, W.79 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.55, A:H.57, A:C.74, A:H.77 FES.13: 7 residues within 4Å: Chain B: C.55, H.57, R.58, C.74, Y.76, H.77, W.79 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.55, B:H.57, B:C.74 FES.21: 8 residues within 4Å: Chain C: C.55, H.57, R.58, C.74, Y.76, H.77, G.78, W.79 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.55, C:H.57, C:C.74, C:H.77

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

CL.9: 2 residues within 4Å: Chain A: H.139, K.140 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: N.11, H.222, P.223 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: Y.13, H.222, P.223, L.224, C.225 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: S.41, H.42, V.67, N.69, N.70 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: H.222, P.223 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain C: S.41, H.42, V.67, N.69, N.70 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: H.93, P.94, D.95, M.96 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Design principles for site-selective hydroxylation by a Rieske oxygenase. Nat Commun (2022)

Release Date

2022-01-19

Peptides

SxtDIOX: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SxtDIOX

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