SMTL ID : 4qeh.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.255, H2O.1 MG.2: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: 32O.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.4: 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.255, H2O.10 MG.5: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: 32O.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.7: 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.255, H2O.20 MG.8: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: 32O.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.10: 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.255, H2O.30 MG.11: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: 32O.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

4 x 32O: beta-L-ribofuranose(Non-covalent)

32O.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, K.289 Ligands: MG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.181, A:H.220, A:K.289 Water bridges: A:N.215 Salt bridges: A:H.54 32O.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, K.289 Ligands: MG.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.181, B:H.220, B:K.289 Water bridges: B:N.215 Salt bridges: B:H.54 32O.9: 11 residues within 4Å: Chain C: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287, K.289 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.181, C:H.220, C:K.289 Water bridges: C:T.90, C:N.215 Salt bridges: C:H.54 32O.12: 11 residues within 4Å: Chain D: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287, K.289 Ligands: MG.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.181, D:H.220, D:K.289 Water bridges: D:T.90, D:N.215 Salt bridges: D:H.54

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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