SMTL ID : 3njz.1

Crystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans Adducts with salicylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.119, H.121, H.160 Ligands: SAL.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.121, A:H.160 FE2.5: 4 residues within 4Å: Chain B: H.119, H.121, H.160 Ligands: SAL.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.121, B:H.160 FE2.9: 4 residues within 4Å: Chain C: H.119, H.121, H.160 Ligands: SAL.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.121, C:H.160 FE2.13: 4 residues within 4Å: Chain D: H.119, H.121, H.160 Ligands: SAL.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.121, D:H.160

4 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.2: 15 residues within 4Å: Chain A: R.83, A.85, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Chain B: L.38, M.46 Ligands: FE2.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.83, A:A.85, A:D.174, A:L.176, A:L.176, A:I.178, B:L.38 Hydrogen bonds: A:H.119 Salt bridges: A:R.83, A:H.119, A:R.127, A:H.160, A:H.162 SAL.6: 15 residues within 4Å: Chain A: L.38, M.46 Chain B: R.83, A.85, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Ligands: FE2.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.83, B:A.85, B:D.174, B:L.176, B:L.176, B:I.178, A:L.38 Hydrogen bonds: B:H.119 Salt bridges: B:R.83, B:H.119, B:R.127, B:H.160, B:H.162 SAL.10: 15 residues within 4Å: Chain C: R.83, A.85, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Chain D: L.38, M.46 Ligands: FE2.9 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:R.83, C:A.85, C:D.174, C:L.176, C:L.176, C:I.178, D:L.38 Hydrogen bonds: C:H.119 Salt bridges: C:R.83, C:H.119, C:R.127, C:H.160, C:H.162 SAL.14: 15 residues within 4Å: Chain C: L.38, M.46 Chain D: R.83, A.85, W.104, Q.108, H.119, H.121, R.127, H.160, H.162, D.174, L.176, I.178 Ligands: FE2.13 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:R.83, D:A.85, D:D.174, D:L.176, D:L.176, D:I.178, C:L.38 Hydrogen bonds: D:H.119 Salt bridges: D:R.83, D:H.119, D:R.127, D:H.160, D:H.162

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.265, E.282, R.295, E.297, R.347 Chain C: L.219 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.265, A:E.282, A:E.297, A:R.347, A:R.347 GOL.4: 5 residues within 4Å: Chain A: P.56, H.57, V.58, M.314, E.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.57, A:V.58 Water bridges: A:M.314 GOL.7: 6 residues within 4Å: Chain B: R.265, E.282, R.295, E.297, R.347 Chain D: L.219 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.265, B:E.282, B:E.297, B:R.347, B:R.347 GOL.8: 5 residues within 4Å: Chain B: P.56, H.57, V.58, M.314, E.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.57, B:V.58 Water bridges: B:M.314 GOL.11: 6 residues within 4Å: Chain A: L.219 Chain C: R.265, E.282, R.295, E.297, R.347 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.265, C:E.282, C:E.297, C:R.347, C:R.347 GOL.12: 5 residues within 4Å: Chain C: P.56, H.57, V.58, M.314, E.317 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.58 Water bridges: C:T.319 GOL.15: 6 residues within 4Å: Chain B: L.219 Chain D: R.265, E.282, R.295, E.297, R.347 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.265, D:E.282, D:E.297, D:R.347, D:R.347 GOL.16: 5 residues within 4Å: Chain D: P.56, H.57, V.58, M.314, E.317 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.58 Water bridges: D:T.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraroni, M. et al., Crystal structures of salicylate 1,2-dioxygenase-substrates adducts: A step towards the comprehension of the structural basis for substrate selection in class III ring cleaving dioxygenases. J.Struct.Biol. (2012)

Release Date

2011-07-13

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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