SMTL ID : 1muw.2 (1 other biounit)

The 0.86 Angstrom Structure of Xylose Isomerase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.86 Å

Oligo State

homo-tetramer

Ligands

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: E.216, H.219, N.246, D.254, D.256 Ligands: OH.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.216, A:H.219, A:D.254, A:D.256, OH.5 MN.2: 6 residues within 4Å: Chain A: E.180, E.216, H.219, D.244, D.286 Ligands: OH.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286, H2O.13 MN.6: 6 residues within 4Å: Chain B: E.216, H.219, N.246, D.254, D.256 Ligands: OH.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.216, B:H.219, B:D.254, B:D.256, OH.10 MN.7: 6 residues within 4Å: Chain B: E.180, E.216, H.219, D.244, D.286 Ligands: OH.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286, H2O.31 MN.11: 6 residues within 4Å: Chain C: E.216, H.219, N.246, D.254, D.256 Ligands: OH.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.216, C:H.219, C:D.254, C:D.256, OH.15 MN.12: 6 residues within 4Å: Chain C: E.180, E.216, H.219, D.244, D.286 Ligands: OH.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286, H2O.48 MN.16: 6 residues within 4Å: Chain D: E.216, H.219, N.246, D.254, D.256 Ligands: OH.20 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:E.216, D:H.219, D:D.254, D:D.256, OH.20 MN.17: 6 residues within 4Å: Chain D: E.180, E.216, H.219, D.244, D.286 Ligands: OH.20 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286, H2O.65

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.162, G.165, L.205, E.206, R.207, Y.211 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.162, A:Y.211, H2O.15 MG.4: 4 residues within 4Å: Chain A: P.35, L.57, H.70, R.73 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.57, A:H.70, H2O.4 MG.8: 6 residues within 4Å: Chain B: D.162, G.165, L.205, E.206, R.207, Y.211 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.162, B:Y.211, H2O.32 MG.9: 4 residues within 4Å: Chain B: P.35, L.57, H.70, R.73 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.57, B:H.70, H2O.21 MG.13: 6 residues within 4Å: Chain C: D.162, G.165, L.205, E.206, R.207, Y.211 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.162, C:Y.211, H2O.49 MG.14: 4 residues within 4Å: Chain C: P.35, L.57, H.70, R.73 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.57, C:H.70, H2O.38 MG.18: 6 residues within 4Å: Chain D: D.162, G.165, L.205, E.206, R.207, Y.211 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.162, D:Y.211, H2O.67 MG.19: 4 residues within 4Å: Chain D: P.35, L.57, H.70, R.73 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.57, D:H.70, H2O.56

4 x OH: HYDROXIDE ION(Non-covalent)

OH.5: 8 residues within 4Å: Chain A: E.216, H.219, D.254, D.256, D.286, K.288 Ligands: MN.1, MN.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.254, A:K.288 OH.10: 8 residues within 4Å: Chain B: E.216, H.219, D.254, D.256, D.286, K.288 Ligands: MN.6, MN.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.254, B:K.288 OH.15: 8 residues within 4Å: Chain C: E.216, H.219, D.254, D.256, D.286, K.288 Ligands: MN.11, MN.12 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.254, C:K.288 OH.20: 8 residues within 4Å: Chain D: E.216, H.219, D.254, D.256, D.286, K.288 Ligands: MN.16, MN.17 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.254, D:K.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenn, T.D. et al., Active Site Dynamics at 0.86A: Crystallographic Analysis of a Metal-Mediated Hydride Shift. To be Published

Release Date

2002-11-06

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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