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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 3ghz

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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 3ghz

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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 3ghz

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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 3ghz

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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

Reference:

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.
Page generated: Mon Dec 14 08:11:23 2020

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