SMTL ID : 3kbv.1

Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NI.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 NI.2: 4 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.7 NI.3: 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 NI.4: 4 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287, H2O.16 NI.5: 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.18 NI.6: 4 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.25 NI.7: 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.26 NI.8: 4 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287, H2O.33

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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