SMTL ID : 3kco.1

Room temperature neutron structure of D-Xylose Isomerase in complex with two Ni2+ cations and d12-D-glucose in the linear form (refined jointly with X-ray structure 3KBN)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 8 residues within 4Å: Chain A: K.183, E.217, H.220, D.255, D.257 Ligands: NI.2, NI.3, GLO.4 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.1 NI.2: 8 residues within 4Å: Chain A: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: NI.1, GLO.4 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 NI.3: 7 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: NI.1, GLO.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 NI.5: 8 residues within 4Å: Chain B: K.183, E.217, H.220, D.255, D.257 Ligands: NI.6, NI.7, GLO.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.217, B:E.217, B:H.220, H2O.12, H2O.12 NI.6: 8 residues within 4Å: Chain B: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: NI.5, GLO.8 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.12, H2O.12 NI.7: 7 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: NI.5, GLO.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 NI.9: 8 residues within 4Å: Chain C: K.183, E.217, H.220, D.255, D.257 Ligands: NI.10, NI.11, GLO.12 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.217, C:E.217, C:H.220, H2O.24, H2O.24 NI.10: 8 residues within 4Å: Chain C: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: NI.9, GLO.12 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.24, H2O.24 NI.11: 7 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: NI.9, GLO.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 NI.13: 8 residues within 4Å: Chain D: K.183, E.217, H.220, D.255, D.257 Ligands: NI.14, NI.15, GLO.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.217, D:E.217, D:H.220, H2O.36, H2O.36 NI.14: 8 residues within 4Å: Chain D: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: NI.13, GLO.16 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.36, H2O.36 NI.15: 7 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: NI.13, GLO.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

4 x GLO: D-glucose(Post Translational Modification)

GLO.4: 20 residues within 4Å: Chain A: W.16, H.54, M.88, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, H.285, D.287 Chain C: F.26 Ligands: NI.1, NI.2, NI.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.16, A:H.54, A:E.181, A:K.183 Water bridges: A:W.137, A:E.181, A:N.215, A:E.217, A:D.287, A:D.287 GLO.8: 20 residues within 4Å: Chain B: W.16, H.54, M.88, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, H.285, D.287 Chain D: F.26 Ligands: NI.5, NI.6, NI.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:W.16, B:H.54, B:E.181, B:K.183 Water bridges: B:W.137, B:E.181, B:N.215, B:E.217, B:D.287, B:D.287 GLO.12: 20 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, M.88, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, H.285, D.287 Ligands: NI.9, NI.10, NI.11 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:W.16, C:H.54, C:E.181, C:K.183 Water bridges: C:W.137, C:E.181, C:N.215, C:E.217, C:D.287, C:D.287 GLO.16: 20 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, M.88, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, H.285, D.287 Ligands: NI.13, NI.14, NI.15 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:W.16, D:H.54, D:E.181, D:K.183, D:D.287, D:D.287 Water bridges: D:W.137, D:E.181, D:E.217, D:D.287, D:D.287, D:D.287

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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