SMTL ID : 3xis.1

A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.1: 11 residues within 4Å: Chain A: W.15, H.53, F.93, V.134, W.136, E.180, E.216, D.244, D.286 Ligands: XLS.2, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.180, A:D.244 Water bridges: A:W.15, A:W.15, A:T.89, A:K.288 Salt bridges: A:H.53 XYS.5: 11 residues within 4Å: Chain B: W.15, H.53, F.93, V.134, W.136, E.180, E.216, D.244, D.286 Ligands: XLS.6, MG.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.180, B:D.244 Water bridges: B:W.15, B:W.15, B:T.89, B:K.288 Salt bridges: B:H.53 XYS.9: 11 residues within 4Å: Chain C: W.15, H.53, F.93, V.134, W.136, E.180, E.216, D.244, D.286 Ligands: XLS.10, MG.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.180 Water bridges: C:W.15, C:W.15, C:K.288 Salt bridges: C:H.53 XYS.13: 11 residues within 4Å: Chain D: W.15, H.53, F.93, V.134, W.136, E.180, E.216, D.244, D.286 Ligands: XLS.14, MG.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.180 Water bridges: D:W.15, D:W.15, D:K.288 Salt bridges: D:H.53

4 x XLS: D-xylose(Non-covalent)

XLS.2: 16 residues within 4Å: Chain A: W.15, H.53, T.89, F.93, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286 Chain C: F.25 Ligands: XYS.1, MG.3, MG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.53, A:T.89 XLS.6: 16 residues within 4Å: Chain B: W.15, H.53, T.89, F.93, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286 Chain D: F.25 Ligands: XYS.5, MG.7, MG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.53, B:T.89 XLS.10: 16 residues within 4Å: Chain A: F.25 Chain C: W.15, H.53, T.89, F.93, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286 Ligands: XYS.9, MG.11, MG.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.53 XLS.14: 16 residues within 4Å: Chain B: F.25 Chain D: W.15, H.53, T.89, F.93, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286 Ligands: XYS.13, MG.15, MG.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.53, D:H.219

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.216, H.219, D.254, D.256 Ligands: XLS.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.216, A:H.219, A:D.254, A:D.256, H2O.5 MG.4: 6 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: XYS.1, XLS.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286 MG.7: 5 residues within 4Å: Chain B: E.216, H.219, D.254, D.256 Ligands: XLS.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.216, B:H.219, B:D.254, B:D.256, H2O.19 MG.8: 6 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: XYS.5, XLS.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286 MG.11: 5 residues within 4Å: Chain C: E.216, H.219, D.254, D.256 Ligands: XLS.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.216, C:H.219, C:D.254, C:D.256, H2O.33 MG.12: 6 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: XYS.9, XLS.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286 MG.15: 5 residues within 4Å: Chain D: E.216, H.219, D.254, D.256 Ligands: XLS.14 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.216, D:H.219, D:D.254, D:D.256, H2O.47 MG.16: 6 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: XYS.13, XLS.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitlow, M. et al., A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose. Proteins (1991)

Release Date

1992-07-15

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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