SMTL ID : 3kbm.1

Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors and d12-D-alpha-glucose in the cyclic form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x CD: CADMIUM ION(Non-covalent)

CD.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.257, H2O.1 CD.2: 6 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 CD.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.257, H2O.9 CD.5: 6 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 CD.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.257, H2O.17 CD.8: 6 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 CD.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.257, H2O.25 CD.11: 6 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.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 GLC: alpha-D-glucopyranose(Non-covalent)

GLC.3: 13 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: CD.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.90 Water bridges: A:W.137, A:N.215 Salt bridges: A:H.54 GLC.6: 13 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: CD.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.90 Water bridges: B:W.137, B:N.215 Salt bridges: B:H.54 GLC.9: 13 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: CD.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.90, C:T.90 Water bridges: C:W.137, C:N.215 Salt bridges: C:H.54 GLC.12: 13 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: CD.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.90, D:T.90 Water bridges: D:W.137, D:N.215 Salt bridges: D:H.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalevsky, A.Y. et al., Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study. Structure (2010)

Release Date

2010-06-16

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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