SMTL ID : 6wnb.1

Structure of the Rieske non-heme iron oxygenase SxtT with dideoxysaxitoxin bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

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

FES.1: 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.11: 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.22: 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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Q.110, R.112, D.126, I.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.112, A:I.127 Water bridges: A:W.12, A:Q.110, A:N.125 GOL.3: 7 residues within 4Å: Chain A: A.92, H.93, P.94, D.95, M.96 Chain B: K.180, V.181 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.95, A:M.96, B:V.181 GOL.12: 3 residues within 4Å: Chain B: R.112, Y.113, W.133 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.113, B:D.134 Water bridges: B:G.114 GOL.13: 4 residues within 4Å: Chain B: Q.288, P.289, A.290, R.291 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.288, B:A.290, B:R.291, B:R.291, B:R.291 GOL.14: 4 residues within 4Å: Chain B: N.70, N.82, Q.83, A.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.70, B:N.82, B:Q.83, B:A.84 GOL.23: 3 residues within 4Å: Chain C: R.112, Y.113, W.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.113 Water bridges: C:E.111, C:G.114 GOL.24: 4 residues within 4Å: Chain C: H.139, G.261, S.262, E.263 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.261, C:S.262, C:E.263

3 x U5A: [(2Z,3aS,4R,6Z,10aR)-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate(Non-covalent)

U5A.4: 13 residues within 4Å: Chain A: S.159, F.165, R.204, N.216, Q.226, C.228, S.230, I.237, D.239, M.255, Y.273, T.276, I.277 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.165 Hydrogen bonds: A:R.204, A:R.204, A:Q.226, A:S.230, A:S.230, A:I.237, A:D.239, A:Y.273, A:Y.273, A:T.276, A:T.276 Water bridges: A:S.159, A:D.280, A:D.280 Salt bridges: A:D.239 U5A.15: 15 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, D.280 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.165 Hydrogen bonds: B:R.204, B:R.204, B:N.216, B:Q.226, B:S.230, B:Y.273, B:T.276, B:T.276 Water bridges: B:N.158, B:S.159, B:D.280, B:D.280 Salt bridges: B:D.239, B:D.280 U5A.25: 11 residues within 4Å: Chain C: S.159, F.165, Q.226, C.228, S.230, I.237, D.239, M.255, Y.273, T.276, I.277 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.165 Hydrogen bonds: C:Q.226, C:S.230, C:I.237, C:Y.273, C:Y.273, C:T.276, C:T.276 Water bridges: C:D.280 Salt bridges: C:D.239

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

FE.5: 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.2, H2O.4 FE.16: 3 residues within 4Å: Chain B: H.164, H.169, D.280 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.164, B:H.169, B:D.280, B:D.280, H2O.8 FE.26: 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.16, H2O.16

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

SO4.6: 2 residues within 4Å: Chain A: N.70, Q.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.70 Water bridges: A:Q.83 SO4.7: 3 residues within 4Å: Chain A: K.187, T.194, G.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.219 Salt bridges: A:K.187 SO4.8: 4 residues within 4Å: Chain A: H.139, G.261, S.262, E.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.263 Salt bridges: A:H.139 SO4.9: 4 residues within 4Å: Chain A: P.23, R.40, Q.44, N.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.45 Water bridges: A:R.40 Salt bridges: A:R.40 SO4.10: 3 residues within 4Å: Chain A: R.30, K.35 Chain B: Q.288 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.30, A:K.35 SO4.17: 2 residues within 4Å: Chain B: P.312, R.315 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.315 SO4.18: 2 residues within 4Å: Chain A: M.64 Chain B: R.282 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.282, B:R.282 Salt bridges: B:R.282 SO4.19: 3 residues within 4Å: Chain B: H.139, K.140, E.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.140, B:E.263 Salt bridges: B:K.140 SO4.20: 2 residues within 4Å: Chain B: H.93 Chain C: K.180 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Water bridges: B:M.96, C:K.180, C:K.180 Salt bridges: B:H.93, C:K.180 SO4.21: 1 residues within 4Å: Chain B: R.80 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.80 SO4.27: 4 residues within 4Å: Chain C: N.70, N.82, Q.83, A.84 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.70, C:Q.83, C:Q.83, C:A.84 SO4.28: 4 residues within 4Å: Chain C: W.217, V.229, E.231, R.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.217 Salt bridges: C:R.236 SO4.29: 3 residues within 4Å: Chain C: H.139, K.140, E.263 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.140, C:E.263, C:E.263 Salt bridges: C:H.139, C:K.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukowski, A.L. et al., Structural basis for divergent C-H hydroxylation selectivity in two Rieske oxygenases. Nat Commun (2020)

Release Date

2020-06-17

Peptides

SxtT: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SxtT

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