SMTL ID : 3ecj.1

Structure of E323L mutant of Homoprotocatechuate 2,3-Dioxygenase from Brevibacterium fuscum at 1.65A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.155, A:H.214, A:E.267, H2O.12, H2O.12, H2O.12 FE2.4: 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.27, H2O.27, H2O.27 FE2.8: 4 residues within 4Å: Chain C: H.155, H.200, 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.41, H2O.42, H2O.42 FE2.12: 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.55, H2O.56, H2O.56

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.6: 4 residues within 4Å: Chain B: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: R.243, H.248, Y.257, R.293 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: I.283, T.284, W.285 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:R.236, C:R.236, A:N.286 Hydrogen bonds: A:T.284 GOL.7: 3 residues within 4Å: Chain B: I.283, T.284, W.285 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Water bridges: D:R.236, B:N.286, B:N.286 Hydrogen bonds: B:T.284 GOL.10: 3 residues within 4Å: Chain C: I.283, T.284, W.285 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:R.236, A:R.236, C:T.284, C:N.286 GOL.11: 6 residues within 4Å: Chain C: S.44, Y.45, H.61, K.110, G.111, T.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.44 Water bridges: C:G.111, C:G.111 GOL.14: 3 residues within 4Å: Chain D: I.283, T.284, W.285 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Water bridges: B:R.236, D:N.286 Hydrogen bonds: D:T.284 GOL.15: 5 residues within 4Å: Chain D: Q.182, D.183, D.184, T.284, N.286 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.183, D:D.184, D:N.286 Water bridges: D:Q.182

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.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovaleva, E.G. et al., Intermediate in the O-O Bond Cleavage Reaction of an Extradiol Dioxygenase. Biochemistry (2008)

Release Date

2008-10-07

Peptides

PROTEIN (Homoprotocatechuate 2,3-dioxygenase): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PROTEIN (Homoprotocatechuate 2,3-dioxygenase)

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