SMTL ID : 2r8z.6 (5 other biounits)

Crystal structure of YrbI phosphatase from Escherichia coli in complex with a phosphate and a calcium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.32, D.34, D.125 Ligands: PO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.32, A:D.34, A:D.125, H2O.3, H2O.5 CA.3: 4 residues within 4Å: Chain B: D.32, D.34, D.125 Ligands: PO4.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.32, B:D.34, B:D.125, H2O.1, H2O.5 CA.5: 4 residues within 4Å: Chain C: D.32, D.34, D.125 Ligands: PO4.6 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.32, C:D.34, C:D.125, H2O.11, H2O.11 CA.7: 4 residues within 4Å: Chain D: D.32, D.34, D.125 Ligands: PO4.8 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.32, D:D.34, D:D.125, H2O.15, H2O.18

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

PO4.2: 9 residues within 4Å: Chain A: D.32, V.33, D.34, T.76, G.77, R.78, K.102 Chain D: S.187 Ligands: CA.1 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:V.33, A:D.34, A:T.76, A:T.76, A:T.76, A:G.77, A:R.78, D:S.187 Salt bridges: A:K.102 Water bridges: D:S.187, D:S.187 PO4.4: 9 residues within 4Å: Chain A: S.187 Chain B: D.32, V.33, D.34, T.76, G.77, R.78, K.102 Ligands: CA.3 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.33, B:D.34, B:D.34, B:T.76, B:T.76, B:G.77, B:R.78 Water bridges: B:D.32, B:T.76, B:K.102, B:K.102, A:S.187, A:S.187, A:S.187 Salt bridges: B:K.102 PO4.6: 10 residues within 4Å: Chain B: S.187 Chain C: D.32, V.33, D.34, I.75, T.76, G.77, R.78, K.102 Ligands: CA.5 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:V.33, C:D.34, C:D.34, C:I.75, C:G.77, C:R.78, B:S.187, B:S.187 Water bridges: C:K.102, C:K.102 Salt bridges: C:K.102 PO4.8: 8 residues within 4Å: Chain D: D.32, V.33, D.34, T.76, G.77, R.78, K.102 Ligands: CA.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:V.33, D:D.34, D:D.34, D:T.76, D:T.76, D:T.76, D:G.77, D:R.78 Water bridges: D:K.102, D:K.102, D:K.102 Salt bridges: D:K.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, T. et al., The Tail of KdsC: CONFORMATIONAL CHANGES CONTROL THE ACTIVITY OF A HALOACID DEHALOGENASE SUPERFAMILY PHOSPHATASE. J.Biol.Chem. (2009)

Release Date

2008-09-23

Peptides

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

D
P

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase

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