SMTL ID : 3lm4.1

Crystal Structure of 2,3-Dihydroxy Biphenyl dioxygenase from Rhodococcus sp. (strain RHA1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: H.156, H.218, Y.259, E.269 Ligands: PEO.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.156, A:H.218, A:E.269, H2O.1, H2O.1 FE.4: 5 residues within 4Å: Chain B: H.156, H.218, Y.259, E.269 Ligands: PEO.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.156, B:H.218, B:E.269, H2O.8, H2O.8 FE.7: 5 residues within 4Å: Chain C: H.156, H.218, Y.259, E.269 Ligands: PEO.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.156, C:H.218, C:E.269, H2O.16, H2O.16 FE.10: 5 residues within 4Å: Chain D: H.156, H.218, Y.259, E.269 Ligands: PEO.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.156, D:H.218, D:E.269, H2O.22, H2O.22

4 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.2: 8 residues within 4Å: Chain A: H.156, N.158, W.193, H.201, A.204, H.218 Ligands: FE.1, HPX.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.158, A:H.201 PEO.5: 8 residues within 4Å: Chain B: H.156, N.158, W.193, H.201, A.204, H.218 Ligands: FE.4, HPX.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.158, B:W.193 Water bridges: B:S.255, B:S.255 PEO.8: 8 residues within 4Å: Chain C: H.156, N.158, W.193, H.201, A.204, H.218 Ligands: FE.7, HPX.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.158, C:W.193 PEO.11: 8 residues within 4Å: Chain D: H.156, N.158, W.193, H.201, A.204, H.218 Ligands: FE.10, HPX.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.158, D:W.193 Water bridges: D:S.255

4 x HPX: (2Z,4E)-2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOIC ACID(Non-covalent)

HPX.3: 13 residues within 4Å: Chain A: N.158, I.190, W.193, M.206, R.207, M.209, H.250, I.252, T.253, G.296, Y.309, F.310 Ligands: PEO.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.190, A:W.193, A:F.310, A:F.310 Hydrogen bonds: A:N.158, A:Y.309 Water bridges: A:Y.309, A:Y.309 Salt bridges: A:H.250 HPX.6: 13 residues within 4Å: Chain B: N.158, I.190, W.193, M.206, R.207, M.209, H.250, I.252, T.253, G.296, Y.309, F.310 Ligands: PEO.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.190, B:I.190, B:W.193, B:Y.309, B:F.310 Hydrogen bonds: B:N.158, B:T.253, B:Y.309, B:Y.309 Water bridges: B:S.255 Salt bridges: B:H.250 HPX.9: 14 residues within 4Å: Chain C: N.158, I.190, W.193, M.206, R.207, M.209, H.250, I.252, T.253, G.296, L.297, Y.309, F.310 Ligands: PEO.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.190, C:W.193, C:Y.309, C:F.310, C:F.310 Hydrogen bonds: C:N.158, C:Y.309 Water bridges: C:Y.309, C:Y.309 Salt bridges: C:H.250 HPX.12: 13 residues within 4Å: Chain D: N.158, I.190, W.193, M.206, R.207, M.209, H.250, I.252, T.253, G.296, Y.309, F.310 Ligands: PEO.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.190, D:I.190, D:W.193, D:F.310, D:F.310 Hydrogen bonds: D:N.158, D:T.253, D:Y.309 Water bridges: D:Y.309, D:Y.309 Salt bridges: D:H.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Syed Ibrahim, B. et al., Crystal Structure of 2,3-Dihydroxy Biphenyl dioxygenase from Rhodococcus sp. (strain RHA1). To be Published

Release Date

2010-02-23

Peptides

Catechol 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catechol 2,3-dioxygenase