SMTL ID : 1rmy.1

Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with deoxycytosine and phosphate bound to the catalytic metal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.44, D.46, T.48, D.167 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.44, A:D.46, A:D.167, H2O.182, H2O.382, H2O.391 MG.2: 6 residues within 4Å: Chain B: D.44, D.46, T.48, D.167, S.168 Ligands: PO4.3 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.44, B:D.46, B:D.167, H2O.768, H2O.787 MG.6: 4 residues within 4Å: Chain C: D.44, D.46, T.48, D.167 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.44, C:D.46, C:D.167, H2O.969, H2O.1169, H2O.1178 MG.7: 6 residues within 4Å: Chain D: D.44, D.46, T.48, D.167, S.168 Ligands: PO4.8 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.44, D:D.46, D:D.167, H2O.1555, H2O.1574

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

PO4.3: 9 residues within 4Å: Chain B: D.44, I.45, D.46, T.112, G.113, R.114, K.152 Ligands: MG.2, DCZ.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:I.45, B:D.46, B:D.46, B:D.46, B:T.112, B:T.112, B:G.113, B:R.114 Water bridges: B:K.152 Salt bridges: B:K.152 PO4.8: 9 residues within 4Å: Chain D: D.44, I.45, D.46, T.112, G.113, R.114, K.152 Ligands: MG.7, DCZ.9 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:I.45, D:D.46, D:D.46, D:D.46, D:D.46, D:T.112, D:G.113, D:R.114 Water bridges: D:K.152 Salt bridges: D:K.152

4 x DCZ: 2'-DEOXYCYTIDINE(Non-covalent)

DCZ.4: 10 residues within 4Å: Chain B: D.46, F.56, Y.70, L.71, W.77, G.113, R.114, T.192, Y.193 Ligands: PO4.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.71, B:Y.193 Hydrogen bonds: B:Y.70, B:G.113, B:T.192, B:T.192 Water bridges: B:D.145, B:K.152, B:T.192 pi-Stacking: B:F.56, B:Y.193 DCZ.5: 9 residues within 4Å: Chain A: D.46, F.56, Y.70, L.71, W.77, G.113, R.114, T.192, Y.193 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.46, A:F.56, A:Y.193 Hydrogen bonds: A:D.46, A:Y.70, A:G.113, A:T.192, A:T.192 Water bridges: A:Y.193 pi-Stacking: A:F.56, A:Y.193 DCZ.9: 10 residues within 4Å: Chain D: D.46, F.56, Y.70, L.71, W.77, G.113, R.114, T.192, Y.193 Ligands: PO4.8 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.71, D:Y.193 Hydrogen bonds: D:G.113, D:T.192 Water bridges: D:D.145, D:K.152, D:T.192, D:T.192 pi-Stacking: D:F.56, D:Y.193 DCZ.10: 9 residues within 4Å: Chain C: D.46, F.56, Y.70, L.71, W.77, G.113, R.114, T.192, Y.193 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:D.46, C:F.56, C:Y.193 Hydrogen bonds: C:D.46, C:Y.70, C:G.113, C:T.192 Water bridges: C:T.192, C:Y.193 pi-Stacking: C:F.56, C:Y.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calderone, V. et al., Insights in the catalytic mechanism of AphA from Escherichia coli. To be Published

Release Date

2004-12-14

Peptides

Class B acid phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Class B acid phosphatase

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