SMTL ID : 4qe5.1

Room temperature X-ray structure of D-xylose isomerase in complex with two Mg2+ ions and L-ribulose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: RUU.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.181, A:E.181, A:E.217, A:D.245, A:D.287 MG.2: 4 residues within 4Å: Chain A: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.1 MG.4: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: RUU.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.181, B:E.181, B:E.217, B:D.245, B:D.287 MG.5: 4 residues within 4Å: Chain B: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.12 MG.7: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: RUU.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.181, C:E.181, C:E.217, C:D.245, C:D.287 MG.8: 4 residues within 4Å: Chain C: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.23 MG.10: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: RUU.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.181, D:E.181, D:E.217, D:D.245, D:D.287 MG.11: 4 residues within 4Å: Chain D: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.34

4 x RUU: alpha-L-ribulofuranose(Non-covalent)

RUU.3: 11 residues within 4Å: Chain A: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.181, A:E.181 Water bridges: A:T.90, A:T.91, A:N.215 RUU.6: 11 residues within 4Å: Chain B: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: MG.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.181, B:E.181 Water bridges: B:T.90, B:T.91, B:N.215 RUU.9: 11 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: MG.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.181, C:E.181 Water bridges: C:T.90, C:T.91, C:N.215 RUU.12: 11 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: MG.10 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.181, D:E.181 Water bridges: D:T.90, D:T.91, D:N.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Langan, P. et al., L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Structure (2014)

Release Date

2014-09-03

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xylose isomerase

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