SMTL ID : 4fag.1

Crystal Structure of the Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans W104Y mutant in complex with gentisate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: H.119, H.121, H.160 Ligands: GTQ.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.121, A:H.160 FE.4: 4 residues within 4Å: Chain B: H.119, H.121, H.160 Ligands: GTQ.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.119, B:H.121, B:H.160 FE.7: 4 residues within 4Å: Chain C: H.119, H.121, H.160 Ligands: GTQ.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.119, C:H.121, C:H.160 FE.10: 4 residues within 4Å: Chain D: H.119, H.121, H.160 Ligands: GTQ.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.119, D:H.121, D:H.160

4 x GTQ: 2,5-dihydroxybenzoic acid(Non-covalent)

GTQ.2: 14 residues within 4Å: Chain A: R.83, A.85, Y.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Chain B: M.46 Ligands: FE.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.83, A:L.176, A:L.176, A:I.178 Hydrogen bonds: A:Y.104, A:D.174 Salt bridges: A:R.83, A:H.119, A:R.127, A:H.160, A:H.162 GTQ.5: 14 residues within 4Å: Chain A: M.46 Chain B: R.83, A.85, Y.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Ligands: FE.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.83, B:L.176, B:L.176, B:I.178 Hydrogen bonds: B:Y.104, B:D.174 Salt bridges: B:R.83, B:H.119, B:R.127, B:H.160, B:H.162 GTQ.8: 14 residues within 4Å: Chain C: R.83, A.85, Y.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Chain D: M.46 Ligands: FE.7 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:R.83, C:L.176, C:L.176, C:I.178 Hydrogen bonds: C:Y.104, C:Y.104, C:D.174, C:D.174 Salt bridges: C:R.83, C:H.119, C:R.127, C:H.160, C:H.162 GTQ.11: 14 residues within 4Å: Chain C: M.46 Chain D: R.83, A.85, Y.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Ligands: FE.10 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:R.83, D:L.176, D:L.176, D:I.178 Hydrogen bonds: D:Y.104, D:Y.104, D:D.174, D:D.174 Salt bridges: D:R.83, D:H.119, D:R.127, D:H.160, D:H.162

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: F.204, E.208, R.209, C.212, H.213, F.237 Chain C: E.244 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.213 Water bridges: A:C.212, C:R.240 GOL.6: 7 residues within 4Å: Chain B: F.204, E.208, R.209, C.212, H.213, F.237 Chain D: E.244 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.213 Water bridges: B:C.212, D:R.240 GOL.9: 7 residues within 4Å: Chain A: E.244 Chain C: F.204, E.208, R.209, C.212, H.213, F.237 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:R.240, C:C.212 Hydrogen bonds: C:H.213 GOL.12: 7 residues within 4Å: Chain B: E.244 Chain D: F.204, E.208, R.209, C.212, H.213, F.237 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:H.213 Water bridges: D:C.212, B:R.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraroni, M. et al., The generation of a 1-hydroxy-2-naphthoate 1,2-dioxygenase by single point mutations of salicylate 1,2-dioxygenase - Rational design of mutants and the crystal structures of the A85H and W104Y variants. J.Struct.Biol. (2012)

Release Date

2012-09-26

Peptides

Gentisate 1,2-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Gentisate 1,2-dioxygenase

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