SMTL ID : 3ojk.1

Structure of Co-substituted Homoprotocatechuate 2,3-Dioxygenase in complex with 4-nitrocatechol at 1.68 Ang resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-tetramer

Ligands

4 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: H.155, H.200, H.214, E.267 Ligands: 4NC.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.155, A:H.214, A:E.267, H2O.8 CO.5: 4 residues within 4Å: Chain B: H.155, H.200, H.214, E.267 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.155, B:H.214, B:E.267, H2O.16, H2O.16, H2O.22 CO.11: 5 residues within 4Å: Chain C: H.155, H.200, H.214, E.267 Ligands: 4NC.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.155, C:H.214, C:E.267, H2O.35 CO.16: 5 residues within 4Å: Chain D: H.155, H.200, H.214, E.267 Ligands: 4NC.17 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.155, D:H.214, D:E.267, H2O.49

3 x 4NC: 4-NITROCATECHOL(Non-covalent)

4NC.2: 15 residues within 4Å: Chain A: H.155, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293 Ligands: CO.1, CL.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.192 Hydrogen bonds: A:V.250, A:Y.257 Water bridges: A:N.157 pi-Stacking: A:H.248 4NC.12: 15 residues within 4Å: Chain C: H.155, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293 Ligands: CO.11, CL.13 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.192 Hydrogen bonds: C:V.250 Water bridges: C:N.157 pi-Stacking: C:H.248 4NC.17: 15 residues within 4Å: Chain D: H.155, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293 Ligands: CO.16, CL.18 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:H.248 Hydrogen bonds: D:V.250 Water bridges: D:N.157 pi-Stacking: D:H.248

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

CL.3: 6 residues within 4Å: Chain A: R.243, H.248, Y.257, R.293, W.304 Ligands: 4NC.2 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain C: R.243, H.248, Y.257, R.293, W.304 Ligands: 4NC.12 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain D: R.243, H.248, Y.257, R.293, W.304 Ligands: 4NC.17 Ligand excluded by PLIP

5 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 13 residues within 4Å: Chain A: E.22, V.24, T.67, K.68, G.69, K.75, R.104, F.108, V.109, L.312, L.314, D.315, G.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.22, A:K.75 Water bridges: A:R.117 P6G.9: 13 residues within 4Å: Chain B: E.22, V.24, T.67, K.68, K.75, R.104, F.108, V.109, R.117, L.312, L.314, D.315, G.316 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.22, B:K.75 Water bridges: B:Q.50, B:R.117 P6G.10: 5 residues within 4Å: Chain B: D.183, D.184, T.284, A.344, G.345 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.286 P6G.15: 14 residues within 4Å: Chain C: E.22, V.24, T.67, K.68, G.69, K.75, R.104, F.108, V.109, R.117, L.312, L.314, D.315, G.316 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.22, C:K.75 Water bridges: C:Q.50, C:R.117 P6G.20: 11 residues within 4Å: Chain D: E.22, V.24, T.67, K.68, K.75, R.104, F.108, V.109, L.312, D.315, G.316 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.22, D:K.75 Water bridges: D:Q.50, D:R.117

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 2 residues within 4Å: Chain B: D.184, E.185 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.184, B:E.185, H2O.16

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 7 residues within 4Å: Chain A: R.82 Chain B: A.12, D.14, D.172, L.173, G.174, R.195 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.82, B:R.82 Hydrogen bonds: B:R.195, B:R.195, B:R.195 PG4.14: 8 residues within 4Å: Chain C: A.12, D.14, D.172, L.173, G.174, R.176, R.195 Chain D: R.82 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.176, C:R.195, C:R.195, C:R.195 PG4.19: 6 residues within 4Å: Chain D: Y.45, H.61, D.106, K.110, G.111, T.133 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.133, D:T.133 Water bridges: D:G.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fielding, A.J. et al., A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase. J.Biol.Inorg.Chem. (2011)

Release Date

2010-12-29

Peptides

Homoprotocatechuate 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Homoprotocatechuate 2,3-dioxygenase

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