SMTL ID : 3eck.1

Structure of E323L Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum in complex with putative O-O bond cleavage intermediate formed via in crystallo reaction with 4-sulfonyl catechol at low oxygen concentrations

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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.13, H2O.13, H2O.13 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: 5 residues within 4Å: Chain C: H.155, H.200, H.214, E.267 Ligands: XXG.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.155, C:H.214, C:E.267, H2O.39 FE2.13: 5 residues within 4Å: Chain D: H.155, H.200, H.214, E.267 Ligands: XXG.15 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.155, D:H.214, D:E.267, H2O.53

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: 6 residues within 4Å: Chain C: R.243, H.248, Y.257, R.293, W.304 Ligands: XXG.10 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain D: R.243, H.248, Y.257, R.293, W.304 Ligands: XXG.15 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 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.284 Water bridges: A:N.286, C:R.236 GOL.7: 3 residues within 4Å: Chain B: I.283, T.284, W.285 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.284 Water bridges: B:N.286, D:R.236 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.12: 4 residues within 4Å: Chain A: R.236 Chain C: I.283, T.284, W.285 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.284, A:R.236 Water bridges: C:N.286 GOL.16: 5 residues within 4Å: Chain D: Q.182, D.183, D.184, T.284, N.286 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.182, D:D.184, D:N.286 GOL.17: 3 residues within 4Å: Chain D: I.283, T.284, W.285 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Water bridges: B:R.236, B:R.236, D:N.286

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.14

2 x XXG: 3,3-dihydroxy-4-oxocyclohexa-1,5-diene-1-sulfonic acid(Non-covalent)

XXG.10: 18 residues within 4Å: Chain C: H.155, N.157, W.192, H.200, H.214, R.243, H.248, G.249, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304 Ligands: FE2.8, CL.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.192, C:H.248, C:V.250 Hydrogen bonds: C:N.157, C:G.249, C:V.250 Water bridges: C:W.192, C:R.293 Salt bridges: C:R.243, C:H.248, C:R.293 XXG.15: 18 residues within 4Å: Chain D: H.155, N.157, W.192, H.200, H.214, R.243, H.248, G.249, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304 Ligands: FE2.13, CL.14 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.192, D:H.248 Hydrogen bonds: D:N.157, D:G.249, D:V.250 Water bridges: D:W.192, D:R.293 Salt bridges: D:R.243, D:H.248, D:R.293

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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