SMTL ID : 1s5n.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 0.95 Å

Oligo State

homo-tetramer

Ligands

4 x XYL: Xylitol(Non-covalent)

XYL.1: 18 residues within 4Å: Chain A: W.15, H.53, T.89, F.93, V.134, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286, K.288 Chain D: F.25 Ligands: MN.2, MN.3, OH.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.15, A:K.182, A:H.219, A:D.286 Water bridges: A:W.136, A:N.214 XYL.7: 18 residues within 4Å: Chain B: W.15, H.53, T.89, F.93, V.134, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286, K.288 Chain C: F.25 Ligands: MN.8, MN.9, OH.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.15, B:K.182, B:H.219, B:D.286 Water bridges: B:W.136, B:N.214 XYL.13: 18 residues within 4Å: Chain B: F.25 Chain C: W.15, H.53, T.89, F.93, V.134, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286, K.288 Ligands: MN.14, MN.15, OH.18 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:W.15, C:K.182, C:H.219, C:D.286 Water bridges: C:W.136, C:N.214 XYL.19: 18 residues within 4Å: Chain A: F.25 Chain D: W.15, H.53, T.89, F.93, V.134, W.136, E.180, K.182, E.216, H.219, D.244, D.254, D.286, K.288 Ligands: MN.20, MN.21, OH.24 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:W.15, D:K.182, D:H.219, D:D.286 Water bridges: D:W.136, D:N.214

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

MN.2: 7 residues within 4Å: Chain A: E.180, E.216, H.219, D.244, D.286 Ligands: XYL.1, OH.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.180, A:E.216, A:D.244, A:D.286 MN.3: 8 residues within 4Å: Chain A: K.182, E.216, H.219, N.246, D.254, D.256 Ligands: XYL.1, OH.6 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.6 MN.8: 7 residues within 4Å: Chain B: E.180, E.216, H.219, D.244, D.286 Ligands: XYL.7, OH.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.180, B:E.216, B:D.244, B:D.286 MN.9: 8 residues within 4Å: Chain B: K.182, E.216, H.219, N.246, D.254, D.256 Ligands: XYL.7, OH.12 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.12 MN.14: 7 residues within 4Å: Chain C: E.180, E.216, H.219, D.244, D.286 Ligands: XYL.13, OH.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.180, C:E.216, C:D.244, C:D.286 MN.15: 8 residues within 4Å: Chain C: K.182, E.216, H.219, N.246, D.254, D.256 Ligands: XYL.13, OH.18 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.58 MN.20: 7 residues within 4Å: Chain D: E.180, E.216, H.219, D.244, D.286 Ligands: XYL.19, OH.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.180, D:E.216, D:D.244, D:D.286 MN.21: 8 residues within 4Å: Chain D: K.182, E.216, H.219, N.246, D.254, D.256 Ligands: XYL.19, OH.24 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.24

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.10: 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:E.206, B:R.207, B:Y.211 NA.11: 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:H.70 Water bridges: B:L.57, B:R.73 NA.16: 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.17: 4 residues within 4Å: Chain C: P.35, L.57, H.70, R.73 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.70 Water bridges: C:D.34, C:L.57, C:R.73 NA.22: 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:D.162, D:E.206, D:R.207 NA.23: 4 residues within 4Å: Chain D: P.35, L.57, H.70, R.73 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.70 Water bridges: D:D.34, D:H.70, D:R.73

4 x OH: HYDROXIDE ION(Non-covalent)

OH.6: 8 residues within 4Å: Chain A: E.216, D.254, D.256, D.286, K.288 Ligands: XYL.1, MN.2, MN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.216 Water bridges: A:K.288 OH.12: 8 residues within 4Å: Chain B: E.216, D.254, D.256, D.286, K.288 Ligands: XYL.7, MN.8, MN.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.216 Water bridges: B:K.288 OH.18: 8 residues within 4Å: Chain C: E.216, D.254, D.256, D.286, K.288 Ligands: XYL.13, MN.14, MN.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.286 Water bridges: C:K.288 OH.24: 8 residues within 4Å: Chain D: E.216, D.254, D.256, D.286, K.288 Ligands: XYL.19, MN.20, MN.21 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.216 Water bridges: D:K.288

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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