SMTL ID : 7sze.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 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: 7 residues within 4Å: Chain B: C.55, H.57, R.58, C.74, Y.76, H.77, 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.21: 7 residues within 4Å: Chain C: C.55, H.57, R.58, C.74, Y.76, H.77, W.79 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.55, C:H.57, C:C.74

3 x 9SL: [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate(Non-covalent)

9SL.2: 10 residues within 4Å: Chain A: S.159, F.165, Q.226, C.228, D.239, M.241, Y.255, D.272, Y.273, V.276 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.159, A:N.216, A:Q.226 Water bridges: A:Q.226, A:D.239, A:Y.255, A:Y.255, A:Y.255, A:D.272, A:D.272, A:D.280 Salt bridges: A:D.239 9SL.13: 12 residues within 4Å: Chain B: S.159, F.165, I.172, N.216, Q.226, C.228, D.239, M.241, Y.255, D.272, Y.273, V.276 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.159, B:N.216, B:Q.226, B:Y.255, B:Y.273 Water bridges: B:N.216, B:Q.226, B:Y.273 Salt bridges: B:D.239 9SL.22: 11 residues within 4Å: Chain C: S.159, F.165, N.216, Q.226, C.228, D.239, M.241, Y.255, D.272, Y.273, V.276 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.159, C:Q.226, C:Y.273 Water bridges: C:N.216, C:N.216, C:Q.226, C:Q.226, C:T.230, C:T.230, C:Y.255, C:Y.255, C:Y.255, C:D.272, C:D.272, C:Y.273 Salt bridges: C:D.239

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: H.139, K.140, K.263 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.140, A:K.140, A:K.263, A:K.263 GOL.4: 4 residues within 4Å: Chain A: P.47, I.48, C.109, E.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.48, A:I.48, A:E.111 Water bridges: A:C.109 GOL.5: 3 residues within 4Å: Chain A: K.144, D.274, E.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.144, A:K.144 GOL.6: 5 residues within 4Å: Chain A: V.88, Q.89, P.94, M.96, V.97 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.88, A:P.94, A:M.96 GOL.7: 5 residues within 4Å: Chain A: E.111, R.112, Y.113, G.114, W.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.113, A:G.114, A:W.133 Water bridges: A:E.111, A:E.111 GOL.14: 2 residues within 4Å: Chain B: E.19, D.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.19, B:D.20 Water bridges: B:K.17 GOL.15: 4 residues within 4Å: Chain B: P.23, R.40, Q.44, N.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.40, B:R.40 GOL.16: 4 residues within 4Å: Chain B: E.248, R.291, T.330, Y.331 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.248, B:R.291 Water bridges: B:T.330 GOL.23: 3 residues within 4Å: Chain C: H.139, K.140, K.263 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.139, C:K.140, C:K.140, C:K.263 GOL.24: 3 residues within 4Å: Chain C: E.248, R.291, T.330 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.291, C:T.330 Water bridges: C:T.330, C:V.333, C:V.333 GOL.25: 3 residues within 4Å: Chain C: K.187, W.217, R.219 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.219 GOL.26: 4 residues within 4Å: Chain C: W.12, H.108, C.109, Q.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.108, C:C.109

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

FE.8: 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.7, H2O.8 FE.17: 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.19, H2O.19 FE.27: 4 residues within 4Å: Chain C: N.158, 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.30, H2O.31

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

CL.9: 5 residues within 4Å: Chain A: S.41, H.42, V.67, N.69, N.70 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: H.93, P.94, D.95, M.96 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: P.23, R.40, Q.44, N.45 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: H.139, K.140 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain B: Y.13, H.222, P.223, L.224, C.225 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: S.41, H.42, V.67, N.69, N.70 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: N.11, H.222, P.223 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain C: R.219, Y.227 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
C

B
A

C
B

SxtDIOX

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