SMTL ID : 4qee.1

Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ ions and L-ribose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain A: E.217, H.220, N.247, 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 NI.2: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: Z6J.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 NI.4: 5 residues within 4Å: Chain B: E.217, H.220, N.247, 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.10 NI.5: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: Z6J.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 NI.7: 5 residues within 4Å: Chain C: E.217, H.220, N.247, 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.20 NI.8: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: Z6J.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 NI.10: 5 residues within 4Å: Chain D: E.217, H.220, N.247, 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.30 NI.11: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: Z6J.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 Z6J: alpha-L-ribofuranose(Non-covalent)

Z6J.3: 10 residues within 4Å: Chain A: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.16 Water bridges: A:N.215 Salt bridges: A:H.54 Z6J.6: 10 residues within 4Å: Chain B: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.16 Water bridges: B:N.215 Salt bridges: B:H.54 Z6J.9: 10 residues within 4Å: Chain C: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.16 Water bridges: C:T.90, C:N.215 Salt bridges: C:H.54 Z6J.12: 10 residues within 4Å: Chain D: W.16, H.54, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.16 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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