Calcium in PDB 1ydy: Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli

All present enzymatic activity of Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli:
3.1.4.46;

The structure of Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli, PDB code: 1ydy was solved by V.N.Malashkevich, E.Fedorov, S.C.Almo, S.K.Burley, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.789, 74.469, 157.219, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.8

The binding sites of Calcium atom in the Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli (pdb code 1ydy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli, PDB code: 1ydy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:25.6 occ:1.00 OE1 A:GLU171 2.3 26.1 1.0 OE1 A:GLU63 2.4 24.1 1.0 O A:HOH1043 2.5 33.3 1.0 O2 A:GOL902 2.5 23.4 1.0 OD1 A:ASP65 2.5 23.1 1.0 O1 A:GOL902 2.5 26.1 1.0 O A:HOH905 2.6 23.2 1.0 CD A:GLU63 3.3 23.1 1.0 C1 A:GOL902 3.4 24.0 1.0 C2 A:GOL902 3.4 23.4 1.0 CG A:ASP65 3.4 22.0 1.0 CD A:GLU171 3.5 28.0 1.0 OD2 A:ASP65 3.7 24.4 1.0 OE2 A:GLU63 3.7 24.0 1.0 C3 A:GOL902 4.0 24.9 1.0 NE2 A:GLN208 4.1 23.3 1.0 CB A:GLU171 4.3 25.5 1.0 OE2 A:GLU171 4.3 25.4 1.0 O A:HOH1185 4.3 45.0 1.0 NE2 A:HIS36 4.3 23.6 1.0 OE1 A:GLN208 4.5 24.3 1.0 CG A:GLU171 4.5 22.7 1.0 CG A:GLU63 4.6 25.0 1.0 CD A:GLN208 4.6 21.1 1.0 CD2 A:HIS36 4.7 24.8 1.0 O3 A:GOL902 4.7 26.5 1.0 CB A:ASP65 4.8 22.8 1.0 O A:HOH1070 4.8 54.4 1.0 NZ A:LYS173 4.8 34.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:22.5 occ:1.00 OE1 B:GLU171 2.3 21.8 1.0 OE1 B:GLU63 2.4 22.2 1.0 O2 B:GOL901 2.4 22.1 1.0 OD1 B:ASP65 2.4 20.3 1.0 O B:HOH906 2.5 21.2 1.0 O1 B:GOL901 2.6 22.2 1.0 O B:HOH1052 2.6 39.6 1.0 C1 B:GOL901 3.4 24.8 1.0 C2 B:GOL901 3.4 23.0 1.0 CG B:ASP65 3.4 20.4 1.0 CD B:GLU63 3.4 19.2 1.0 CD B:GLU171 3.5 18.8 1.0 OD2 B:ASP65 3.6 23.3 1.0 OE2 B:GLU63 3.8 21.1 1.0 C3 B:GOL901 4.0 22.7 1.0 OE2 B:GLU171 4.2 23.4 1.0 NE2 B:GLN208 4.2 18.9 1.0 CB B:GLU171 4.3 17.8 1.0 NE2 B:HIS36 4.3 22.4 1.0 OE1 B:GLN208 4.5 22.0 1.0 CG B:GLU171 4.5 19.0 1.0 CG B:GLU63 4.6 19.0 1.0 CD B:GLN208 4.6 20.7 1.0 O3 B:GOL901 4.6 24.2 1.0 NZ B:LYS173 4.6 33.7 1.0 CD2 B:HIS78 4.7 32.0 1.0 CD2 B:HIS36 4.7 22.5 1.0 O B:HOH1104 4.7 34.8 1.0 CB B:ASP65 4.8 22.4 1.0

V.M.Malashkevich, E.Fedorov, S.C.Almo. Crystal Structure of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli To Be Published.