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Magnesium in PDB 3t80: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine

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

Protein crystallography data

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine, PDB code: 3t80 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), B.L.Staker, T.E.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 200.013, 147.657, 56.919, 90.00, 106.38, 90.00
R / Rfree (%) 21.1 / 24.5

Other elements in 3t80:

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine (pdb code 3t80). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine, PDB code: 3t80:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3t80

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Magnesium binding site 1 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.6
occ:1.00
 OD1 A:ASP8 2.3 44.1 1.0
O A:HOH188 2.5 59.9 1.0
O C:HOH177 2.6 78.6 1.0
OG1 C:THR132 2.6 47.6 1.0
ZN A:ZN301 3.3 80.1 1.0
CG A:ASP8 3.3 41.1 1.0
OD2 A:ASP8 3.9 42.6 1.0
CB C:THR132 3.9 45.8 1.0
CB A:ASP8 4.3 39.3 1.0
O C:THR133 4.4 43.8 1.0
CD1 A:ILE57 4.4 60.1 1.0
O5' C:CTN401 4.4 60.4 1.0
CA A:ASP8 4.5 39.3 1.0
N C:THR133 4.7 46.1 1.0
CG2 C:THR133 4.7 48.3 1.0
N A:VAL9 4.7 41.0 1.0
O A:PHE7 4.7 41.9 1.0
CA C:THR132 4.8 44.8 1.0
CG2 C:THR132 4.8 44.4 1.0
O A:VAL9 4.9 45.5 1.0

Magnesium binding site 2 out of 8 in 3t80

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Magnesium binding site 2 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg160

b:66.1
occ:1.00
 OD1 B:ASP8 3.0 48.8 1.0
ZN B:ZN301 3.3 86.3 1.0
OE2 A:GLU135 3.3 66.7 1.0
OG1 A:THR132 3.9 45.4 1.0
O A:THR133 4.1 43.1 1.0
CD A:GLU135 4.1 62.4 1.0
O B:VAL9 4.2 47.9 1.0
CG B:ASP8 4.2 43.9 1.0
O5' A:CTN401 4.4 42.5 1.0
CE1 B:HIS10 4.4 55.2 1.0
OD2 B:ASP8 4.6 45.6 1.0
CG A:GLU135 4.7 57.4 1.0
OG1 A:THR133 4.8 43.2 1.0
NE2 B:HIS10 4.8 55.2 1.0
OE1 A:GLU135 4.9 71.0 1.0
O B:HOH175 5.0 65.7 1.0

Magnesium binding site 3 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 3 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg160

b:39.2
occ:1.00
 OE2 B:GLU149 1.6 57.9 1.0
OE2 A:GLU149 2.0 55.0 1.0
OE1 C:GLU149 2.2 51.1 1.0
OE2 C:GLU149 2.2 59.6 1.0
CD C:GLU149 2.4 51.5 1.0
CD A:GLU149 2.5 47.2 1.0
OE1 A:GLU149 2.5 49.3 1.0
CD B:GLU149 2.5 52.2 1.0
OE1 B:GLU149 2.9 59.6 1.0
CG C:GLU149 3.8 50.4 1.0
CG A:GLU149 3.9 45.0 1.0
CG B:GLU149 3.9 51.5 1.0
NE2 A:HIS5 4.4 43.2 1.0
NE2 C:HIS5 4.5 44.1 1.0
NE2 B:HIS5 4.7 41.4 1.0
CE1 A:HIS5 4.7 44.9 1.0
CE1 B:HIS5 4.9 44.1 1.0
CB C:GLU149 4.9 46.1 1.0
CB A:GLU149 5.0 41.6 1.0

Magnesium binding site 4 out of 8 in 3t80

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Magnesium binding site 4 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:58.4
occ:1.00
 O B:HOH179 2.3 55.7 1.0
OD1 C:ASP8 2.3 46.9 1.0
O B:HOH183 2.4 69.2 1.0
OG1 B:THR132 2.7 48.0 1.0
CG C:ASP8 3.3 44.4 1.0
ZN C:ZN301 3.5 81.2 1.0
O5' B:CTN401 3.9 60.6 1.0
CB B:THR132 3.9 45.0 1.0
OD2 C:ASP8 4.0 46.0 1.0
CB C:ASP8 4.3 43.9 1.0
CD1 C:ILE57 4.4 65.3 1.0
O C:PHE7 4.6 50.0 1.0
O B:THR133 4.6 46.5 1.0
CA C:ASP8 4.6 44.0 1.0
CA B:THR132 4.7 43.6 1.0
N C:VAL9 4.9 44.5 1.0
N B:THR133 4.9 44.2 1.0
C5' B:CTN401 4.9 55.2 1.0
CG2 B:THR132 4.9 43.1 1.0

Magnesium binding site 5 out of 8 in 3t80

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Magnesium binding site 5 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:50.2
occ:1.00
 OD1 D:ASP8 2.4 46.5 1.0
O D:HOH173 2.4 67.2 1.0
O D:HOH180 2.6 56.7 1.0
OG1 F:THR132 2.7 51.0 1.0
O F:HOH179 3.3 52.7 1.0
CG D:ASP8 3.4 41.8 1.0
ZN D:ZN301 3.7 72.8 1.0
OD2 D:ASP8 4.0 43.0 1.0
CB F:THR132 4.0 47.8 1.0
O5' F:CTN401 4.1 49.9 1.0
O F:THR133 4.4 47.1 1.0
CB D:ASP8 4.5 40.8 1.0
O D:VAL9 4.7 42.9 1.0
OE2 F:GLU135 4.7 60.0 1.0
N F:THR133 4.7 45.4 1.0
CA D:ASP8 4.8 41.0 1.0
N D:VAL9 4.8 39.1 1.0
CA F:THR132 4.8 46.2 1.0
CG2 F:THR132 5.0 46.5 1.0
NE2 D:HIS10 5.0 51.2 1.0
O D:PHE7 5.0 41.9 1.0

Magnesium binding site 6 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 6 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg160

b:45.1
occ:1.00
 OE2 F:GLU149 1.9 61.0 1.0
OE1 E:GLU149 2.2 56.1 1.0
OE1 D:GLU149 2.2 51.5 1.0
CD F:GLU149 2.4 56.0 1.0
OE1 F:GLU149 2.4 56.0 1.0
OE2 E:GLU149 2.6 57.7 1.0
CD E:GLU149 2.6 54.4 1.0
CD D:GLU149 2.7 52.4 1.0
OE2 D:GLU149 2.8 56.7 1.0
CG F:GLU149 3.8 54.0 1.0
CG E:GLU149 4.0 53.0 1.0
CG D:GLU149 4.0 49.1 1.0
NE2 F:HIS5 4.6 49.6 1.0
NE2 E:HIS5 4.7 49.6 1.0
NE2 D:HIS5 4.7 49.9 1.0
CE1 F:HIS5 4.8 51.9 1.0
CB F:GLU149 5.0 49.3 1.0

Magnesium binding site 7 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 7 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:50.9
occ:1.00
 OD1 E:ASP8 2.4 58.6 1.0
O E:HOH163 2.7 59.3 1.0
OG1 D:THR132 2.9 51.4 1.0
ZN E:ZN301 3.2 71.0 1.0
CG E:ASP8 3.5 56.7 1.0
OD2 E:ASP8 4.0 58.4 1.0
O5' D:CTN401 4.1 44.1 1.0
CB D:THR132 4.2 50.0 1.0
OE2 D:GLU135 4.2 71.8 1.0
O D:THR133 4.3 54.5 1.0
CB E:ASP8 4.6 54.5 1.0
CD1 E:ILE57 4.7 76.4 1.0
O E:VAL9 4.7 56.1 1.0
N E:VAL9 4.8 52.4 1.0
CA E:ASP8 4.9 52.5 1.0
N D:THR133 4.9 50.1 1.0
CE1 E:HIS10 5.0 66.2 1.0
CA D:THR132 5.0 48.9 1.0

Magnesium binding site 8 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 8 out of 8 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:63.0
occ:1.00
 OD1 F:ASP8 1.9 59.2 1.0
OG1 E:THR132 2.9 55.1 1.0
CG F:ASP8 3.1 55.0 1.0
ZN F:ZN301 3.3 0.4 1.0
OD2 F:ASP8 3.9 56.6 1.0
CB E:THR132 4.0 55.1 1.0
CA F:ASP8 4.1 52.0 1.0
O E:THR133 4.1 51.6 1.0
CB F:ASP8 4.1 51.6 1.0
N F:VAL9 4.1 53.4 1.0
O F:HOH164 4.4 58.5 1.0
O F:PHE7 4.4 53.0 1.0
O F:VAL9 4.4 61.2 1.0
OE2 E:GLU135 4.5 61.9 1.0
C F:ASP8 4.7 52.1 1.0
CG2 E:THR132 4.8 54.5 1.0
N E:THR133 4.9 55.8 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), B.L.Staker, T.E.Edwards. Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine To Be Published.
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