SMTL ID : 4xis.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 Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

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

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

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

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

MN.3: 5 residues within 4Å: Chain A: E.216, H.219, D.254, D.256 Ligands: XLS.1 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.13 MN.4: 6 residues within 4Å: Chain A: E.180, E.216, D.244, D.286 Ligands: XLS.1, XYS.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286 MN.7: 5 residues within 4Å: Chain B: E.216, H.219, D.254, D.256 Ligands: XLS.5 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.29 MN.8: 6 residues within 4Å: Chain B: E.180, E.216, D.244, D.286 Ligands: XLS.5, XYS.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286 MN.11: 5 residues within 4Å: Chain C: E.216, H.219, D.254, D.256 Ligands: XLS.9 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.44 MN.12: 6 residues within 4Å: Chain C: E.180, E.216, D.244, D.286 Ligands: XLS.9, XYS.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286 MN.15: 5 residues within 4Å: Chain D: E.216, H.219, D.254, D.256 Ligands: XLS.13 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.59 MN.16: 6 residues within 4Å: Chain D: E.180, E.216, D.244, D.286 Ligands: XLS.13, XYS.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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