SMTL ID : 4z6t.1

Structure of H200N variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-sulfonyl catechol at 1.50 Ang resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

FE2.1: 3 residues within 4Å: Chain A: H.155, H.214, E.267 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.155, A:H.214, A:E.267, H2O.1, H2O.9, H2O.12 FE2.4: 3 residues within 4Å: Chain B: H.155, 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.17, H2O.26, H2O.28 FE2.10: 4 residues within 4Å: Chain C: H.155, H.214, E.267 Ligands: 4SX.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.40 FE2.14: 3 residues within 4Å: Chain D: H.155, H.214, E.267 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.155, D:H.214, D:E.267, H2O.51, H2O.58, H2O.62

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

P6G.2: 11 residues within 4Å: Chain A: E.22, V.24, T.67, K.68, G.69, K.75, R.104, F.108, L.312, D.315, G.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.22, A:K.75 Water bridges: A:Q.50, A:R.117 P6G.6: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.22, B:K.75 Water bridges: B:Q.50, B:R.104, B:R.104, B:R.117 P6G.7: 6 residues within 4Å: Chain B: Q.182, D.183, D.184, T.284, A.344, G.345 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.286 P6G.11: 13 residues within 4Å: Chain C: E.22, V.24, T.67, K.68, G.69, K.75, R.104, F.108, 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.15: 12 residues within 4Å: Chain D: E.22, V.24, T.67, K.68, K.75, R.104, F.108, V.109, R.117, 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

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

CL.3: 4 residues within 4Å: Chain A: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.243, H.248, R.293 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain C: R.243, H.248, R.293, W.304 Ligands: 4SX.12 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: R.243, H.248, R.293 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.28

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

PG4.9: 8 residues within 4Å: Chain A: R.82 Chain B: A.12, P.13, D.14, D.172, L.173, G.174, R.195 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.172, B:R.195, B:R.195, B:R.195 PG4.17: 5 residues within 4Å: Chain D: Y.45, H.61, K.110, G.111, T.133 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.133 Water bridges: D:G.111

1 x 4SX: 3,4-dihydroxybenzenesulfonic acid(Non-covalent)

4SX.12: 15 residues within 4Å: Chain C: H.155, W.192, H.214, R.243, H.248, G.249, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293 Ligands: FE2.10, CL.13 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.250 Hydrogen bonds: C:G.249, C:V.250, C:R.292 Water bridges: C:N.157, C:N.200 Salt bridges: C:R.243, C:H.248, C:R.293 pi-Stacking: C:H.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovaleva, E.G. et al., Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Biochemistry (2015)

Release Date

2015-08-26

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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