Magnesium in PDB 3ghz: 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium

All present enzymatic activity of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium:
4.6.1.12;

The structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium, PDB code: 3ghz was solved by J.Osipiuk, M.Gu, S.Peterson, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.00 / 2.03
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	143.974, 143.974, 143.974, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.5

The binding sites of Magnesium atom in the 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium (pdb code 3ghz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium, PDB code: 3ghz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:36.9 occ:1.00 OD1 A:ASP8 2.0 27.6 1.0 O C:HOH214 2.0 25.2 1.0 O C:HOH215 2.1 23.7 1.0 O A:HOH198 2.2 27.5 1.0 O A:HOH165 2.2 36.8 1.0 O A:HOH205 2.2 29.0 1.0 CG A:ASP8 3.1 28.4 1.0 OD2 A:ASP8 3.6 32.1 1.0 OG1 C:THR132 4.1 30.9 1.0 OE2 C:GLU135 4.2 31.6 1.0 O A:HOH191 4.2 29.7 1.0 O C:HOH200 4.2 30.9 1.0 NE2 A:HIS10 4.2 32.7 1.0 O A:VAL9 4.2 28.0 1.0 O A:HOH189 4.3 28.7 1.0 CB A:ASP8 4.3 27.5 1.0 O C:THR133 4.3 26.9 1.0 O A:HOH202 4.4 32.7 1.0 O1 A:GOL303 4.5 44.5 1.0 C2 A:GOL303 4.6 48.8 1.0 O2 A:GOL303 4.6 45.9 1.0 CE1 A:HIS10 4.6 37.3 1.0 N A:VAL9 4.6 26.9 1.0 CG2 C:THR133 4.6 25.4 0.6 ND1 A:HIS42 4.7 33.4 1.0 CA A:ASP8 4.7 27.1 1.0 OG1 C:THR133 4.7 27.5 0.4 CD2 A:HIS10 4.9 33.0 1.0 N C:THR133 5.0 27.2 1.0

Magnesium binding site 2 out of 4 in the 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:54.6 occ:1.00 OE1 C:GLU149 2.2 35.4 1.0 OE1 B:GLU149 2.3 38.9 1.0 OE2 B:GLU149 2.3 46.0 1.0 OE1 A:GLU149 2.4 37.5 1.0 OE2 A:GLU149 2.4 45.4 1.0 CD B:GLU149 2.6 38.7 1.0 CD C:GLU149 2.7 36.2 1.0 OE2 C:GLU149 2.7 41.9 1.0 CD A:GLU149 2.7 39.6 1.0 CG B:GLU149 4.0 37.1 1.0 CG C:GLU149 4.0 36.0 1.0 CG A:GLU149 4.2 37.5 1.0 NE2 C:HIS5 4.3 29.8 1.0 NE2 A:HIS5 4.4 29.6 1.0 NE2 B:HIS5 4.5 32.3 1.0 CE1 C:HIS5 4.8 32.0 1.0 CE1 A:HIS5 4.9 32.9 1.0 CD1 C:PHE7 4.9 35.2 1.0 CD1 A:PHE7 5.0 34.3 1.0 CE1 B:HIS5 5.0 33.6 1.0

Magnesium binding site 3 out of 4 in the 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg306 b:35.6 occ:0.60 O B:HOH182 1.9 27.0 1.0 O A:HOH181 1.9 42.9 1.0 O A:HOH167 1.9 33.5 1.0 O B:HOH180 1.9 26.9 1.0 OD1 B:ASP8 2.0 29.4 1.0 O A:HOH176 2.2 33.0 1.0 CG B:ASP8 3.2 27.9 1.0 OD2 B:ASP8 3.7 28.5 1.0 OE2 A:GLU135 4.0 38.0 1.0 NE2 B:HIS10 4.1 33.1 1.0 O B:VAL9 4.2 29.2 1.0 CE1 B:HIS10 4.3 35.9 1.0 OG1 A:THR132 4.3 37.2 1.0 O B:HOH175 4.3 37.0 1.0 CB B:ASP8 4.4 27.6 1.0 O A:HOH177 4.4 34.1 1.0 O A:THR133 4.5 29.4 1.0 N B:VAL9 4.6 27.9 1.0 CG2 A:THR133 4.6 27.9 0.4 CA B:ASP8 4.7 28.1 1.0 ND1 B:HIS42 4.8 30.2 1.0 CD2 B:HIS10 4.9 34.3 1.0

Magnesium binding site 4 out of 4 in the 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg305 b:42.5 occ:1.00 OD1 C:ASP8 1.9 27.3 1.0 O C:HOH218 1.9 28.8 1.0 O C:HOH273 2.1 28.3 1.0 O B:HOH271 2.1 28.1 1.0 O B:HOH272 2.1 29.8 1.0 O C:HOH160 2.1 35.8 1.0 CG C:ASP8 3.0 28.4 1.0 OD2 C:ASP8 3.5 32.0 1.0 O C:HOH208 4.1 31.9 1.0 OE2 B:GLU135 4.2 33.9 1.0 O B:HOH221 4.2 35.4 1.0 O C:VAL9 4.2 27.6 1.0 O C:HOH239 4.2 36.4 1.0 NE2 C:HIS10 4.2 27.1 1.0 OG1 B:THR132 4.2 37.0 1.0 CB C:ASP8 4.3 29.7 1.0 O B:THR133 4.4 33.1 1.0 O3 C:GOL302 4.4 51.0 1.0 CE1 C:HIS10 4.4 29.6 1.0 O2 C:GOL302 4.5 46.7 1.0 N C:VAL9 4.5 28.9 1.0 C2 C:GOL302 4.6 48.4 1.0 CA C:ASP8 4.7 28.9 1.0 ND1 C:HIS42 4.7 33.8 1.0 CG2 B:THR133 4.8 35.7 1.0 C3 C:GOL302 4.9 49.9 1.0 CD2 C:HIS10 5.0 28.4 1.0

J.Osipiuk, M.Gu, S.Peterson, W.F.Anderson, A.Joachimiak. X-Ray Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium. To Be Published.