SMTL ID : 7szh.1

Structure of the Rieske Non-heme Iron Oxygenase SxtT with beta-saxitoxinol Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-trimer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: C.55, H.57, R.58, V.60, 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.12: 9 residues within 4Å: Chain B: C.55, H.57, R.58, V.60, C.74, Y.76, H.77, G.78, W.79 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.55, B:H.57, B:C.74, B:H.77 FES.27: 9 residues within 4Å: Chain C: C.55, H.57, R.58, V.60, 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

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: K.22, P.23, R.40, Q.44, N.45 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: H.139, K.140, E.263 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: W.12, Q.110, R.112, D.126, I.127 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: A.92, H.93, P.94, D.95, M.96 Chain B: K.180 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: S.63, M.64 Chain B: R.282 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: N.70, N.82, Q.83, A.84 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain B: Y.107, H.108, C.109 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain B: N.69, R.80 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: P.94 Chain B: R.176, N.177, Y.178, T.179, K.180 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: E.111, R.112, Y.113, W.133 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: P.47, I.48, C.109, Q.110, E.111 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: P.23, R.40, Q.44, N.45 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: P.131, E.132, Y.227, R.236 Ligand excluded by PLIP GOL.21: 2 residues within 4Å: Chain B: R.30, K.35 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain C: H.139, G.261, S.262, E.263 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain C: R.112, Y.113, W.133 Ligand excluded by PLIP GOL.30: 2 residues within 4Å: Chain C: H.139, K.140 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: L.173, W.214, S.230, E.272, Y.273 Ligands: D82.32 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain C: N.70, N.82, Q.83, A.84 Ligand excluded by PLIP GOL.34: 2 residues within 4Å: Chain C: P.312, R.315 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain C: K.22, P.23, R.40, Q.44, N.45 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain C: K.197, W.217 Ligands: SO4.38 Ligand excluded by PLIP

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

D82.6: 15 residues within 4Å: Chain A: S.159, F.165, L.173, R.204, N.216, Q.226, C.228, V.229, S.230, I.237, D.239, M.255, Y.273, T.276, I.277 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.204, A:R.204, A:Q.226, A:S.230, A:I.237, A:D.239, A:Y.273, A:Y.273, A:T.276, A:T.276 Water bridges: A:Y.198, A:D.280, A:D.280 Salt bridges: A:D.239 D82.22: 14 residues within 4Å: Chain B: S.159, F.165, L.173, F.200, R.204, N.216, Q.226, C.228, S.230, D.239, M.255, Y.273, T.276, I.277 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.216, B:Q.226, B:S.230, B:S.230, B:Y.273, B:T.276, B:T.276 Water bridges: B:S.159, B:R.204, B:Q.226, B:D.280 Salt bridges: B:D.239 D82.32: 14 residues within 4Å: Chain C: S.159, F.165, Q.226, C.228, V.229, S.230, I.237, V.238, D.239, M.255, Y.273, T.276, I.277 Ligands: GOL.31 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Y.198, C:Y.198, C:Q.226, C:I.237, C:D.239, C:Y.273, C:Y.273, C:T.276, C:T.276 Water bridges: C:D.280, C:D.280 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.164, A:H.169, A:D.280, A:D.280, H2O.4 FE.23: 3 residues within 4Å: Chain B: 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.17, H2O.17 FE.37: 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.27, H2O.28

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

SO4.8: 1 residues within 4Å: Chain A: W.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.133 SO4.24: 1 residues within 4Å: Chain B: R.315 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.315 SO4.25: 2 residues within 4Å: Chain B: H.139, K.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.140 Water bridges: B:E.263 Salt bridges: B:K.140 SO4.26: 4 residues within 4Å: Chain B: H.139, G.261, S.262, E.263 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.263 Salt bridges: B:H.139 SO4.38: 5 residues within 4Å: Chain C: W.217, V.229, E.231, R.236 Ligands: GOL.36 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.217 Water bridges: C:R.236 Salt bridges: C:K.197, C:R.236 SO4.39: 2 residues within 4Å: Chain C: N.69, R.80 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.69 Salt bridges: C:R.80

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

CL.9: 1 residues within 4Å: Chain A: H.139 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: H.108, C.109 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

SxtT: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SxtT

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