SMTL ID : 5nhb.1

Crystal structure of xylose isomerase from Piromyces E2 in complex with two Fe2+ ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

8 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: E.233, E.269, D.297, D.340 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.233, A:E.233, A:E.269, A:D.297, A:D.340 FE2.2: 5 residues within 4Å: Chain A: E.269, H.272, D.308, D.310, D.340 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.269, A:E.269, A:H.272, A:D.308, H2O.2 FE2.5: 5 residues within 4Å: Chain B: E.233, E.269, D.297, D.340 Ligands: FE2.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.233, B:E.269, B:D.297, B:D.340, H2O.8 FE2.6: 5 residues within 4Å: Chain B: E.269, H.272, D.308, D.340 Ligands: FE2.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.269, B:H.272, B:D.308, H2O.6, H2O.6 FE2.7: 5 residues within 4Å: Chain C: E.233, E.269, D.297, D.340 Ligands: FE2.8 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.233, C:E.269, C:D.297, C:D.340, H2O.12 FE2.8: 6 residues within 4Å: Chain C: E.269, H.272, D.308, D.310, D.340 Ligands: FE2.7 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.269, C:E.269, C:H.272, C:D.308, H2O.11 FE2.10: 4 residues within 4Å: Chain D: E.233, E.269, D.297, D.340 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.233, D:E.269, D:D.297, D:D.340, H2O.16 FE2.11: 6 residues within 4Å: Chain D: K.235, E.269, H.272, D.308, D.310, D.340 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.269, D:H.272, D:D.308, H2O.18

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: S.112, I.113 Chain B: G.417, E.418 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.418, B:E.418, A:I.113 Water bridges: A:R.150, A:R.166 SO4.4: 5 residues within 4Å: Chain A: G.417, E.418 Chain B: N.111, S.112, I.113 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.111, B:I.113 SO4.9: 5 residues within 4Å: Chain C: N.111, S.112, I.113 Chain D: G.417, E.418 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.418, D:E.418, C:I.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, M. et al., Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography. Biochemistry (2017)

Release Date

2017-11-01

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Xylose isomerase

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