SMTL ID : 4qe4.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 7 residues within 4Å: Chain A: E.217, H.220, D.255, D.257, D.287 Ligands: NI.2, 34V.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.217, A:E.217, A:H.220, H2O.1, H2O.3 NI.2: 6 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: NI.1, 34V.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: 7 residues within 4Å: Chain B: E.217, H.220, D.255, D.257, D.287 Ligands: NI.5, 34V.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.217, B:E.217, B:H.220, H2O.11, H2O.13 NI.5: 6 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: NI.4, 34V.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: 7 residues within 4Å: Chain C: E.217, H.220, D.255, D.257, D.287 Ligands: NI.8, 34V.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.217, C:E.217, C:H.220, H2O.21, H2O.23 NI.8: 6 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: NI.7, 34V.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: 7 residues within 4Å: Chain D: E.217, H.220, D.255, D.257, D.287 Ligands: NI.11, 34V.12 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.217, D:E.217, D:H.220, H2O.31, H2O.33 NI.11: 6 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: NI.10, 34V.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 34V: beta-L-ribulofuranose(Non-covalent)

34V.3: 12 residues within 4Å: Chain A: W.16, H.54, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.1, NI.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.287 Water bridges: A:W.137, A:E.181, A:N.215 34V.6: 12 residues within 4Å: Chain B: W.16, H.54, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.4, NI.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.287 Water bridges: B:W.137, B:E.181, B:N.215 34V.9: 12 residues within 4Å: Chain C: W.16, H.54, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.7, NI.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.90, C:D.287 Water bridges: C:W.137, C:E.181, C:N.215, C:D.257 34V.12: 12 residues within 4Å: Chain D: W.16, H.54, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: NI.10, NI.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.90, D:D.287 Water bridges: D:W.137, D:E.181, D:N.215, D:D.257

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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