SMTL ID : 5zyc.1

Crystal Structure of Glucose Isomerase Soaked with Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 6 residues within 4Å: Chain A: D.9, E.276, R.284, Y.310, L.311, K.314 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.284, A:Y.310 Hydrogen bonds: A:D.9, A:E.276 Salt bridges: A:R.284, A:K.314 ACT.5: 6 residues within 4Å: Chain B: D.9, E.276, R.284, Y.310, L.311, K.314 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.284, B:Y.310 Hydrogen bonds: B:D.9, B:E.276 Salt bridges: B:R.284, B:K.314 ACT.9: 6 residues within 4Å: Chain C: D.9, E.276, R.284, Y.310, L.311, K.314 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:R.284, C:Y.310 Hydrogen bonds: C:E.276 Salt bridges: C:R.284, C:K.314 ACT.13: 6 residues within 4Å: Chain D: D.9, E.276, R.284, Y.310, L.311, K.314 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:R.284, D:Y.310 Hydrogen bonds: D:E.276 Salt bridges: D:R.284, D:K.314

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

MN.2: 4 residues within 4Å: Chain A: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.3 MN.3: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: EDO.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.7 MN.6: 4 residues within 4Å: Chain B: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.16 MN.7: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: EDO.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287, H2O.20 MN.10: 4 residues within 4Å: Chain C: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.29 MN.11: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: EDO.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.33 MN.14: 4 residues within 4Å: Chain D: E.217, H.220, D.255, D.257 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.42 MN.15: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: EDO.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287, H2O.47

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.54 Water bridges: A:T.90, A:N.215 EDO.8: 7 residues within 4Å: Chain B: H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.54 Water bridges: B:T.90, B:N.215 EDO.12: 7 residues within 4Å: Chain C: H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.54 Water bridges: C:N.215 EDO.16: 7 residues within 4Å: Chain D: H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MN.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.54, D:D.287 Water bridges: D:N.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bae, J.E. et al., Structural analysis of substrate recognition by glucose isomerase in Mn2+binding mode at M2 site in S. rubiginosus. Biochem. Biophys. Res. Commun. (2018)

Release Date

2018-11-28

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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