SMTL ID : 117e.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 8 residues within 4Å: Chain A: D.115, E.117, D.120, D.152, K.154 Ligands: MN.2, MN.4, PO4.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.115, A:E.117, A:D.120, A:D.152, H2O.1 MN.2: 4 residues within 4Å: Chain A: E.117, D.120 Ligands: MN.1, PO4.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.117, A:D.120, H2O.1, H2O.1, H2O.1 MN.3: 3 residues within 4Å: Chain A: R.78 Ligands: PO4.5, PO4.6 No protein-ligand interaction detected (PLIP) MN.4: 7 residues within 4Å: Chain A: D.147, D.152, K.154, Y.192 Ligands: MN.1, PO4.5, PO4.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.147, A:D.152, H2O.1, H2O.1 MN.7: 8 residues within 4Å: Chain B: D.115, E.117, D.120, D.152, K.154 Ligands: MN.8, MN.10, PO4.11 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.9 MN.8: 5 residues within 4Å: Chain B: Y.93, E.117, D.120 Ligands: MN.7, PO4.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.117, B:D.120, H2O.9, H2O.9, H2O.9 MN.9: 4 residues within 4Å: Chain B: K.56, E.58, E.117 Ligands: PO4.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.58, B:E.117, H2O.9, H2O.9, H2O.10 MN.10: 5 residues within 4Å: Chain B: D.147, D.152, K.154 Ligands: MN.7, PO4.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.147, B:D.152, H2O.9, H2O.9, H2O.10

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

PO4.5: 8 residues within 4Å: Chain A: K.56, R.78, D.147, Y.192, K.193 Ligands: MN.3, MN.4, PO4.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.192 Water bridges: A:K.56, A:K.73, A:R.78 Salt bridges: A:K.56, A:R.78, A:K.193 PO4.6: 12 residues within 4Å: Chain A: K.56, Y.93, D.115, E.117, D.120, D.152, K.154 Ligands: MN.1, MN.2, MN.3, MN.4, PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.93 Water bridges: A:K.56, A:E.58, A:R.78, A:E.117, A:K.154, A:K.154 Salt bridges: A:K.56, A:K.154 PO4.11: 13 residues within 4Å: Chain B: K.56, E.58, Y.93, D.115, E.117, D.120, D.152, K.154, Y.192 Ligands: MN.7, MN.8, MN.9, MN.10 9 PLIP interactions: 9 interactions with chain B Water bridges: B:K.56, B:K.56, B:K.56, B:K.56, B:K.56, B:K.154, B:Y.192 Salt bridges: B:K.56, B:K.154

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)

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