SMTL ID : 4lnc.1

Neutron structure of the cyclic glucose bound Xylose Isomerase E186Q mutant

Coordinates

PDB Format

Method

NEUTRON DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

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

GLC.1: 16 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.287 Chain C: F.26 Ligands: MN.3, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.220, A:H.220 Water bridges: A:W.16, A:W.16, A:T.90, A:W.137, A:E.217, A:H.220, A:D.255 Salt bridges: A:H.54 GLC.5: 16 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: MN.7, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.220, B:H.220 Water bridges: B:W.16, B:W.16, B:T.90, B:W.137, B:D.255, B:D.255, B:D.257 Salt bridges: B:H.54 GLC.9: 16 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.287 Ligands: MN.11, MG.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:H.220, C:H.220 Water bridges: C:W.16, C:W.16, C:T.90, C:W.137, C:D.255, C:D.255, C:D.257 Salt bridges: C:H.54 GLC.13: 16 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.287 Ligands: MN.15, MG.16 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:H.220, D:H.220 Water bridges: D:W.16, D:W.16, D:T.90, D:W.137, D:D.255, D:D.255, D:D.257 Salt bridges: D:H.54

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

MN.2: 6 residues within 4Å: Chain A: K.183, E.217, H.220, N.247, D.255, D.257 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.10, H2O.10 MN.3: 7 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.1, MG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MN.6: 6 residues within 4Å: Chain B: K.183, E.217, H.220, N.247, D.255, D.257 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.21, H2O.21 MN.7: 7 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.5, MG.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MN.10: 6 residues within 4Å: Chain C: K.183, E.217, H.220, N.247, D.255, D.257 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.33, H2O.33 MN.11: 7 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.9, MG.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MN.14: 6 residues within 4Å: Chain D: K.183, E.217, H.220, N.247, D.255, D.257 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.44, H2O.44 MN.15: 7 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.13, MG.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 7 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.1, MN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.8: 7 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.5, MN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.12: 7 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.9, MN.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.16: 7 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: GLC.13, MN.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munshi, P. et al., Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-02-12

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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