SMTL ID : 5bwg.1

Structure of H200C variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.75 Ang resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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.8, H2O.9 FE2.5: 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.14, H2O.23, H2O.23 FE2.12: 3 residues within 4Å: Chain C: H.155, H.214, E.267 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.155, C:H.214, C:E.267, H2O.31, H2O.37, H2O.38 FE2.15: 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.43, H2O.51, H2O.52

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

CL.2: 4 residues within 4Å: Chain A: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP

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

P6G.3: 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.8: 12 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, D.315, G.316 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.22, B:K.75 Water bridges: B:Q.50 P6G.9: 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.14: 10 residues within 4Å: Chain C: E.22, V.24, T.67, K.68, K.75, R.104, F.108, R.117, D.315, G.316 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.22, C:K.75 Water bridges: C:Q.50 P6G.17: 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 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.22, D:K.75 Water bridges: D:R.117

3 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.4: 9 residues within 4Å: Chain A: I.283, T.284, W.285, D.289, F.341, T.342, R.343, A.344 Chain C: R.236 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Water bridges: C:R.236, C:R.236, A:A.344 Salt bridges: C:R.236 Hydrogen bonds: A:A.344 MPO.10: 8 residues within 4Å: Chain B: I.283, W.285, D.289, F.341, T.342, R.343, A.344 Chain D: R.236 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:A.344 Water bridges: D:R.236, D:R.236 Salt bridges: D:R.236 MPO.11: 9 residues within 4Å: Chain B: R.236 Chain D: I.283, T.284, W.285, D.289, F.341, T.342, R.343, A.344 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:A.344 Water bridges: D:D.289, B:R.236, B:R.236 Salt bridges: B:R.236

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meier, K.K. et al., A Long-Lived Fe(III)-(Hydroperoxo) Intermediate in the Active H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Characterization by Mossbauer, Electron Paramagnetic Resonance, and Density Functional Theory Methods. Inorg.Chem. (2015)

Release Date

2015-10-28

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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