SMTL ID : 4ghd.1

Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with HPCA at 1.85 Ang resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.155, H.200, H.214, E.267 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.155, A:H.214, A:E.267, H2O.9, H2O.9 FE2.5: 4 residues within 4Å: Chain B: H.155, H.200, H.214, E.267 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.155, B:H.214, B:E.267, H2O.21, H2O.22 FE2.11: 5 residues within 4Å: Chain C: H.155, H.200, H.214, E.267 Ligands: DHY.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.155, C:H.214, C:E.267, H2O.32 FE2.15: 4 residues within 4Å: Chain D: H.155, H.200, 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.44, H2O.45, H2O.45

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

P6G.2: 12 residues within 4Å: Chain A: E.22, V.24, T.67, K.68, K.75, R.104, F.108, V.109, L.312, L.314, 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.7: 11 residues within 4Å: Chain B: E.22, V.24, T.67, K.68, K.75, R.104, F.108, 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:R.117 P6G.8: 7 residues within 4Å: Chain B: Q.182, D.183, D.184, T.284, F.341, A.344, G.345 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.286, B:N.286 P6G.12: 12 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:E.22, C:K.75 Water bridges: C:Q.50, C:R.117 P6G.16: 11 residues within 4Å: Chain D: E.22, V.24, T.67, K.68, K.75, R.104, F.108, L.312, L.314, 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 CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: R.243, H.248, R.293, W.304 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: R.243, H.248, R.293 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain D: R.243, H.248, R.293 Ligand excluded by PLIP

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

PG4.4: 8 residues within 4Å: Chain A: A.12, P.13, D.14, D.172, L.173, G.174, R.195 Chain B: R.82 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.82, A:R.195, A:R.195 PG4.9: 7 residues within 4Å: Chain A: R.82 Chain B: A.12, P.13, D.14, D.172, G.174, R.195 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.172, B:R.195, B:R.195, B:R.195 Water bridges: B:R.82 PG4.14: 8 residues within 4Å: Chain C: A.12, D.14, E.171, D.172, L.173, G.174, R.195 Chain D: R.82 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.195, C:R.195 Water bridges: C:I.15

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain B: D.184, E.185 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.184, B:E.185

1 x DHY: 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID(Non-covalent)

DHY.13: 14 residues within 4Å: Chain C: H.155, W.192, H.200, H.214, R.243, H.248, V.250, S.251, F.257, E.267, Y.269, R.293, W.304 Ligands: FE2.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.192, C:V.250, C:R.293 Water bridges: C:N.157 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 the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Biochemistry (2012)

Release Date

2012-10-31

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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