SMTL ID : 3kcl.1

Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x CD: CADMIUM ION(Non-covalent)

CD.1: 6 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.1, 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: 6 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.8, H2O.8 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: 6 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.9 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.16, H2O.16 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: 6 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 Ligands: GLC.12 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.23, H2O.23 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(Post Translational Modification)

GLC.3: 16 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, A.136, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: CD.1, CD.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.90, A:E.181 Water bridges: A:H.54, A:N.215, A:E.217, A:D.257, A:D.287 Salt bridges: A:H.54 GLC.6: 16 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, A.136, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: CD.4, CD.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.90, B:E.181 Water bridges: B:H.54, B:N.215, B:E.217, B:D.257, B:D.287 Salt bridges: B:H.54 GLC.9: 16 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, T.90, F.94, V.135, A.136, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: CD.7, CD.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.90, C:E.181 Water bridges: C:H.54, C:N.215, C:E.217, C:D.257, C:D.287 Salt bridges: C:H.54 GLC.12: 16 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, T.90, F.94, V.135, A.136, W.137, E.181, N.215, E.217, H.220, D.245, D.287 Ligands: CD.10, CD.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.90, D:E.181 Water bridges: D:H.54, D:N.215, D:E.217, D:D.257, D:D.287 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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