Magnesium in PDB 3rf6: Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae

The structure of Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae, PDB code: 3rf6 was solved by B.Nocek, K.Kuznetsova, E.Evdokimova, A.Savchenko, A.Iakunine, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.24 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.912, 71.652, 195.428, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.4

The binding sites of Magnesium atom in the Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae (pdb code 3rf6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae, PDB code: 3rf6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:32.7 occ:0.72 O3P A:G3P501 2.1 38.9 0.8 O A:HOH404 2.2 28.5 1.0 O A:ASP21 2.2 31.9 1.0 OD1 A:ASP298 2.3 30.5 1.0 O A:HOH548 2.4 28.2 1.0 CG A:ASP298 3.1 36.7 1.0 OD2 A:ASP298 3.2 29.8 1.0 C A:ASP21 3.3 28.4 1.0 P A:G3P501 3.5 27.1 0.8 O A:HOH522 3.7 30.7 1.0 CB A:ASP21 3.9 25.5 1.0 C3 A:G3P501 3.9 40.0 0.8 CA A:ASP21 4.0 26.6 1.0 O1P A:G3P501 4.1 28.6 0.8 N A:ASP21 4.2 25.7 1.0 CB A:ALA19 4.3 31.2 1.0 N A:GLY22 4.3 29.6 1.0 OD2 A:ASP303 4.3 32.9 1.0 O2P A:G3P501 4.4 33.6 0.8 O A:HOH555 4.4 37.9 1.0 O4P A:G3P501 4.4 29.8 0.8 CB A:ASP298 4.5 30.2 1.0 CA A:GLY22 4.5 26.8 1.0 N A:ASP298 4.8 32.8 1.0 C A:ILE20 5.0 27.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg353 b:19.1 occ:1.00 O A:GLY134 2.4 17.1 1.0 O A:HOH405 2.4 18.5 1.0 OE1 B:GLN139 2.4 15.5 1.0 O A:HOH385 2.4 17.4 1.0 O B:GLY134 2.5 19.4 1.0 OE1 A:GLN139 2.5 19.2 1.0 C B:GLY134 3.2 17.7 1.0 C A:GLY134 3.2 15.1 1.0 CD B:GLN139 3.2 17.6 1.0 CD A:GLN139 3.3 17.4 1.0 NE2 B:GLN139 3.4 19.6 1.0 NE2 A:GLN139 3.4 23.3 1.0 CA B:LEU135 3.8 16.5 1.0 CA A:LEU135 3.9 14.1 1.0 N B:LEU135 3.9 16.3 1.0 N A:LEU135 3.9 15.6 1.0 CA B:GLY134 4.0 16.5 1.0 N B:SER136 4.1 16.2 1.0 CA A:GLY134 4.1 16.4 1.0 N A:SER136 4.1 18.3 1.0 O B:HOH406 4.2 20.6 1.0 C B:LEU135 4.3 16.9 1.0 C A:LEU135 4.4 17.2 1.0 CG B:GLN139 4.7 15.9 1.0 O B:HOH367 4.8 20.4 1.0 CG A:GLN139 4.8 17.5 1.0 O A:HOH366 4.8 19.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:31.5 occ:0.80 O4P B:G3P501 2.0 27.4 0.8 O B:ASP21 2.2 24.5 1.0 O B:HOH587 2.2 24.2 1.0 OD1 B:ASP298 2.2 23.4 1.0 O B:HOH380 2.3 25.0 1.0 CG B:ASP298 3.0 23.1 1.0 OD2 B:ASP298 3.1 24.1 1.0 C B:ASP21 3.3 21.8 1.0 P B:G3P501 3.5 23.3 0.8 O B:HOH438 3.6 26.9 1.0 CB B:ASP21 3.9 19.4 1.0 C3 B:G3P501 4.0 35.5 0.8 CA B:ASP21 4.0 20.7 1.0 O1P B:G3P501 4.1 30.4 0.8 O3P B:G3P501 4.3 28.5 0.8 N B:ASP21 4.3 18.9 1.0 CB B:ALA19 4.3 22.2 1.0 N B:GLY22 4.3 19.7 1.0 OD2 B:ASP303 4.4 22.6 1.0 O B:HOH421 4.4 34.2 1.0 O2P B:G3P501 4.4 24.3 0.8 CB B:ASP298 4.4 20.3 1.0 CA B:GLY22 4.6 22.0 1.0 N B:ASP298 4.7 21.5 1.0 CG2 B:VAL23 4.9 24.3 1.0

B.Nocek, K.Kuznetsova, E.Evdokimova, A.Savchenko, A.Iakunine, A.Joachimiak. Crystal Structure of Glycerol-3 Phosphate Bound Had-Like Phosphatase From Saccharomyces Cerevisiae To Be Published.