Magnesium in PDB 3l12: Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution

The structure of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution, PDB code: 3l12 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.28 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.409, 136.411, 50.548, 90.00, 118.00, 90.00
R / Rfree (%)	15.6 / 18.7

The structure of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution (pdb code 3l12). 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 Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution, PDB code: 3l12:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution


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 Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg313 b:12.0 occ:1.00 OE1 A:GLU148 2.0 7.7 1.0 OD1 A:ASP51 2.1 8.9 1.0 O A:HOH327 2.1 6.4 1.0 OE2 A:GLU49 2.1 8.0 1.0 O A:HOH353 2.1 8.4 1.0 O4 A:UNL317 2.2 7.3 1.0 CG A:ASP51 3.1 7.7 1.0 CD A:GLU148 3.1 8.9 1.0 CD A:GLU49 3.1 7.8 1.0 O3 A:UNL317 3.4 15.8 1.0 OE1 A:GLU49 3.4 7.2 1.0 OD2 A:ASP51 3.4 7.8 1.0 O6 A:UNL317 3.6 8.7 1.0 O A:HOH593 3.8 32.0 1.0 O2 A:UNL317 3.8 19.7 1.0 O1 A:UNL317 3.9 12.4 1.0 O5 A:UNL317 3.9 18.1 1.0 CB A:GLU148 3.9 6.5 1.0 OE2 A:GLU148 3.9 10.1 1.0 CG A:GLU148 4.0 7.4 1.0 NE2 A:HIS22 4.1 7.8 1.0 O A:HOH617 4.4 19.3 1.0 CB A:ASP51 4.4 7.7 1.0 CG A:GLU49 4.5 6.2 1.0 ND1 A:HIS64 4.6 19.2 0.5 NE A:ARG23 4.6 7.2 1.0 NH2 A:ARG23 4.6 9.6 1.0 CD2 A:HIS22 4.7 8.4 1.0 O A:PHE50 4.8 6.8 1.0 C A:PHE50 4.9 8.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution


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 Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg313 b:11.2 occ:1.00 OE1 B:GLU148 2.0 10.8 1.0 OE2 B:GLU49 2.1 7.8 1.0 OD1 B:ASP51 2.1 9.6 1.0 O B:HOH364 2.1 10.6 1.0 O B:HOH323 2.1 7.3 1.0 O4 B:UNL317 2.1 9.0 1.0 CG B:ASP51 3.1 9.0 1.0 CD B:GLU49 3.1 7.5 1.0 CD B:GLU148 3.2 10.1 1.0 OD2 B:ASP51 3.4 8.4 1.0 O3 B:UNL317 3.4 18.2 1.0 OE1 B:GLU49 3.4 8.2 1.0 O1 B:UNL317 3.6 10.3 1.0 O5 B:UNL317 3.9 17.4 1.0 CB B:GLU148 4.0 9.8 1.0 OE2 B:GLU148 4.0 10.8 1.0 O2 B:UNL317 4.1 18.1 1.0 O B:HOH483 4.1 17.5 1.0 NE2 B:HIS22 4.1 6.9 1.0 CG B:GLU148 4.1 8.6 1.0 O6 B:UNL317 4.2 12.7 1.0 NZ B:LYS150 4.3 6.5 0.4 CB B:ASP51 4.4 9.1 1.0 CG B:GLU49 4.5 7.7 1.0 ND1 B:HIS64 4.5 13.7 1.0 O B:HOH444 4.6 14.0 1.0 CD2 B:HIS22 4.7 6.6 1.0 NE B:ARG23 4.7 6.9 1.0 C B:PHE50 4.9 8.9 1.0 O B:PHE50 4.9 8.7 1.0 CA B:ASP51 5.0 8.8 1.0 N B:ASP51 5.0 6.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution


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 Putative Glycerophosphoryl Diester Phosphodiesterase (YP_165505.1) From Silicibacter Pomeroyi Dss-3 at 1.60 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg314 b:15.8 occ:0.75 NE2 B:HIS79 2.0 14.7 1.0 CE1 B:HIS79 3.0 13.6 1.0 CD2 B:HIS79 3.0 12.4 1.0 O B:HOH624 4.0 33.3 1.0 O B:GLN77 4.1 12.6 0.2 ND1 B:HIS79 4.1 14.7 1.0 CG B:HIS79 4.2 12.5 1.0 O B:GLN77 4.3 13.5 0.8 CB B:GLN77 4.8 19.7 0.8 CB B:GLN77 4.9 13.7 0.2

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.