SMTL ID : 2ik4.1

Yeast inorganic pyrophosphatase variant D117E with magnesium and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.115, D.120, D.152 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.115, A:D.120, A:D.152, H2O.1, H2O.1, H2O.1 MG.2: 1 residues within 4Å: Chain A: D.120 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.3: 8 residues within 4Å: Chain B: D.115, E.117, D.120, D.152, K.154 Ligands: MG.4, MG.5, PO4.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.115, B:E.117, B:D.120, B:D.152, H2O.7 MG.4: 5 residues within 4Å: Chain B: Y.93, E.117, D.120 Ligands: MG.3, PO4.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.117, B:D.120, H2O.7, H2O.7, H2O.7 MG.5: 7 residues within 4Å: Chain B: D.115, D.147, D.152, K.154, Y.192 Ligands: MG.3, PO4.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.147, B:D.152, H2O.7, H2O.7, H2O.7

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 11 residues within 4Å: Chain B: K.56, E.58, Y.93, D.115, E.117, D.120, D.152, K.154 Ligands: MG.3, MG.4, MG.5 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.58, B:Y.93 Water bridges: B:E.48, B:K.56, B:R.78, B:D.115, B:D.152, B:K.154, B:K.154, B:Y.192, B:Y.192, B:Y.192, B:Y.192, B:Y.192 Salt bridges: B:K.56, B:K.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oksanen, E. et al., A Complete Structural Description of the Catalytic Cycle of Yeast Pyrophosphatase. Biochemistry (2007)

Release Date

2007-02-13

Peptides

Inorganic pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Inorganic pyrophosphatase

Related Entries With Identical Sequence