SMTL ID : 2iga.1

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.155, H.200, H.214, E.267 Ligands: XXP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.155, A:H.214, A:E.267, H2O.1 FE2.6: 5 residues within 4Å: Chain B: H.155, H.200, H.214, E.267 Ligands: XX3.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.155, B:H.214, B:E.267 FE2.16: 6 residues within 4Å: Chain C: H.155, H.200, H.214, E.267 Ligands: XX2.18, OXY.19 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.155, C:H.214, C:E.267 FE2.23: 5 residues within 4Å: Chain D: H.155, H.200, H.214, E.267 Ligands: XX3.25 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.155, D:H.214, D:E.267

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

CL.2: 6 residues within 4Å: Chain A: R.243, H.248, Y.257, R.293, W.304 Ligands: XXP.3 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: R.243, H.248, R.293 Ligands: XX3.9 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain C: R.243, H.248, Y.257, R.293 Ligands: XX2.18 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain D: R.243, H.248, Y.257, R.293, W.304 Ligands: XX3.25 Ligand excluded by PLIP

1 x XXP: 2-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC ACID(Non-covalent)

XXP.3: 17 residues within 4Å: Chain A: H.155, N.157, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304 Ligands: FE2.1, CL.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.192 Hydrogen bonds: A:N.157, A:Y.257, A:R.292, A:R.293 Salt bridges: A:H.155, A:H.200, A:H.214, A:H.248

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.243, G.244, Y.255, N.298, P.299, V.301 Chain C: N.298 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.298, A:G.244, A:Y.255 Water bridges: A:N.298 GOL.5: 3 residues within 4Å: Chain A: I.283, T.284, W.285 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.284, C:R.236 Water bridges: A:N.286, C:R.236 GOL.10: 6 residues within 4Å: Chain B: R.243, G.244, N.298, P.299, V.301 Chain D: N.298 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.244, B:Y.255, B:Y.255, B:N.298, D:N.298 GOL.11: 6 residues within 4Å: Chain B: D.289, F.341, T.342, R.343, A.344 Chain D: R.236 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.289, B:A.344 GOL.12: 3 residues within 4Å: Chain B: K.75, R.104, F.108 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.75, B:R.104, B:F.108 Water bridges: B:R.117, B:R.117, B:D.315 GOL.13: 3 residues within 4Å: Chain B: I.283, T.284, W.285 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Water bridges: D:R.236, B:N.286 Hydrogen bonds: B:T.284 GOL.14: 5 residues within 4Å: Chain B: A.12, P.13, D.14, G.174, R.195 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.195 Water bridges: B:A.12 GOL.15: 5 residues within 4Å: Chain B: S.44, Y.45, H.61, K.110, T.133 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.44 GOL.20: 7 residues within 4Å: Chain A: N.298 Chain C: R.243, G.244, Y.255, N.298, P.299, V.301 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.244, C:Y.255, C:Y.255, A:N.298 Water bridges: C:N.298 GOL.21: 6 residues within 4Å: Chain C: V.24, T.67, K.68, G.69, K.75, L.312 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.68, C:K.75 GOL.22: 3 residues within 4Å: Chain C: I.283, T.284, W.285 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.284 Water bridges: C:N.286 GOL.26: 8 residues within 4Å: Chain B: N.298 Chain D: R.243, G.244, Y.255, D.294, N.298, P.299, V.301 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.244, D:Y.255, D:D.294, B:N.298 Water bridges: D:N.298 GOL.27: 5 residues within 4Å: Chain D: T.26, D.27, K.30, P.261, D.262 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.26 Water bridges: D:T.26, D:D.27

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 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 XX3: (1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA-3,5-DIENE(Non-covalent)

XX3.9: 17 residues within 4Å: Chain B: H.155, N.157, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304 Ligands: FE2.6, CL.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.250 Hydrogen bonds: B:N.157, B:Y.257 XX3.25: 17 residues within 4Å: Chain D: H.155, N.157, W.192, H.200, H.214, R.243, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304 Ligands: FE2.23, CL.24 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.250 Hydrogen bonds: D:N.157

1 x XX2: 1-KETO,2-HYDROXY,4-NITROBENZENE, 1 ELECTRON OXIDIZED(Non-covalent)

XX2.18: 16 residues within 4Å: Chain C: H.155, W.192, H.200, H.214, H.248, V.250, S.251, Y.257, E.267, Y.269, R.292, R.293, W.304 Ligands: FE2.16, CL.17, OXY.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.292

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.19: 8 residues within 4Å: Chain C: H.155, N.157, W.192, H.200, A.203, H.214 Ligands: FE2.16, XX2.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovaleva, E.G. et al., Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science (2007)

Release Date

2007-04-24

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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