SMTL ID : 8prk.1

THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.116, D.148, D.153, K.155 Ligands: MN.3, PO4.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.148, A:D.153 MN.2: 4 residues within 4Å: Chain A: Y.94, D.121 Ligands: MN.3, PO4.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.121, H2O.1, H2O.1, H2O.1 MN.3: 6 residues within 4Å: Chain A: D.116, D.121, D.153 Ligands: MN.1, MN.2, PO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.116, A:D.121, A:D.153, H2O.1 MN.5: 7 residues within 4Å: Chain B: D.116, D.121, D.153, K.155 Ligands: MN.6, MN.7, PO4.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.116, B:D.121, B:D.153, H2O.8 MN.6: 5 residues within 4Å: Chain B: D.148, D.153, K.155 Ligands: MN.5, PO4.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.148, B:D.153, H2O.8 MN.7: 4 residues within 4Å: Chain B: Y.94, D.121 Ligands: MN.5, PO4.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.121, H2O.8, H2O.8, H2O.8

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

PO4.4: 10 residues within 4Å: Chain A: K.57, Y.94, D.116, D.118, D.121, D.153, K.155 Ligands: MN.1, MN.2, MN.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.94, A:D.121 Water bridges: A:K.57, A:K.57, A:K.57, A:E.59, A:Y.94 Salt bridges: A:K.57, A:K.155 PO4.8: 10 residues within 4Å: Chain B: K.57, Y.94, D.116, D.118, D.121, D.153, K.155 Ligands: MN.5, MN.6, MN.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.118 Water bridges: B:K.57, B:K.57, B:K.57, B:K.57 Salt bridges: B:K.57, B:K.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tuominen, V. et al., The R78K and D117E active-site variants of Saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implications. J.Mol.Biol. (1998)

Release Date

1998-12-23

Peptides

PROTEIN (INORGANIC PYROPHOSPHATASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (INORGANIC PYROPHOSPHATASE)