SMTL ID : 3bza.1

Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.7 Ang resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.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.1, H2O.1, H2O.1 MN.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.13, H2O.13, H2O.13 MN.9: 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.26, H2O.27, H2O.27 MN.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.38, H2O.38, H2O.38

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.10: 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 A, 2 interactions with chain C Hydrogen bonds: A:T.284 Water bridges: A:N.286, C:R.236, C:R.236 GOL.7: 8 residues within 4Å: Chain B: R.243, G.244, Y.255, D.294, N.298, P.299, V.301 Chain D: N.298 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.244, B:D.294, D:N.298 Water bridges: B:N.298 GOL.8: 4 residues within 4Å: Chain B: I.283, T.284, W.285 Chain D: R.236 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.284, D:R.236 GOL.11: 3 residues within 4Å: Chain C: I.283, T.284, W.285 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:W.285 Water bridges: C:N.286, A:R.236 GOL.14: 3 residues within 4Å: Chain D: I.283, T.284, W.285 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:N.286, B:R.236 GOL.15: 8 residues within 4Å: Chain B: N.298 Chain D: R.243, G.244, Y.255, D.294, N.298, P.299, V.301 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.244, D:D.294, B:N.298 Water bridges: D:N.298

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.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Emerson, J.P. et al., Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-05-13

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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