SMTL ID : 1s5m.1

Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.98 Å

Oligo State

homo-tetramer

Ligands

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 14 residues within 4Å: Chain A: W.15, H.53, M.87, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286 Chain D: F.25 Ligands: MN.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.53 Water bridges: A:W.15, A:W.15, A:W.136, A:N.214, A:D.254, A:D.256 Salt bridges: A:H.53 GLC.6: 14 residues within 4Å: Chain B: W.15, H.53, M.87, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286 Chain C: F.25 Ligands: MN.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.53 Water bridges: B:W.15, B:W.15, B:W.136, B:N.214, B:D.254, B:D.256 Salt bridges: B:H.53 GLC.11: 14 residues within 4Å: Chain B: F.25 Chain C: W.15, H.53, M.87, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.53 Water bridges: C:W.15, C:W.15, C:W.136, C:N.214, C:D.254, C:D.256 Salt bridges: C:H.53 GLC.16: 14 residues within 4Å: Chain A: F.25 Chain D: W.15, H.53, M.87, T.89, F.93, V.134, W.136, E.180, E.216, H.219, D.244, D.286 Ligands: MN.17 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.53 Water bridges: D:W.15, D:W.15, D:W.136, D:N.214, D:D.254, D:D.256 Salt bridges: D:H.53

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

MN.2: 6 residues within 4Å: Chain A: E.180, E.216, H.219, D.244, D.286 Ligands: GLC.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286 MN.3: 6 residues within 4Å: Chain A: K.182, E.216, H.219, N.246, D.254, D.256 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.16 MN.7: 6 residues within 4Å: Chain B: E.180, E.216, H.219, D.244, D.286 Ligands: GLC.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286 MN.8: 6 residues within 4Å: Chain B: K.182, E.216, H.219, N.246, D.254, D.256 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.32 MN.12: 6 residues within 4Å: Chain C: E.180, E.216, H.219, D.244, D.286 Ligands: GLC.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286 MN.13: 6 residues within 4Å: Chain C: K.182, E.216, H.219, N.246, D.254, D.256 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.48 MN.17: 6 residues within 4Å: Chain D: E.180, E.216, H.219, D.244, D.286 Ligands: GLC.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286 MN.18: 6 residues within 4Å: Chain D: K.182, E.216, H.219, N.246, D.254, D.256 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.64

8 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: D.162, G.165, L.205, E.206, R.207, Y.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162, A:D.162, A:E.206, A:R.207 NA.5: 4 residues within 4Å: Chain A: P.35, L.57, H.70, R.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.57, A:H.70 Water bridges: A:R.73 NA.9: 6 residues within 4Å: Chain B: D.162, G.165, L.205, E.206, R.207, Y.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.162, B:D.162, B:E.206, B:R.207 NA.10: 4 residues within 4Å: Chain B: P.35, L.57, H.70, R.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.57, B:H.70 Water bridges: B:R.73 NA.14: 6 residues within 4Å: Chain C: D.162, G.165, L.205, E.206, R.207, Y.211 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.206, C:R.207, C:Y.211 NA.15: 4 residues within 4Å: Chain C: P.35, L.57, H.70, R.73 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.57, C:H.70 Water bridges: C:R.73 NA.19: 6 residues within 4Å: Chain D: D.162, G.165, L.205, E.206, R.207, Y.211 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.206, D:R.207, D:Y.211 NA.20: 4 residues within 4Å: Chain D: P.35, L.57, H.70, R.73 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.57, D:H.70 Water bridges: D:R.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenn, T.D. et al., Xylose isomerase in substrate and inhibitor michaelis States: atomic resolution studies of a metal-mediated hydride shift(,). Biochemistry (2004)

Release Date

2004-02-10

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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