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Magnesium in PDB 3fpi: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate, PDB code: 3fpi was solved by Y.Kim, N.Maltseva, J.Stam, W.F.Anderson, A.Joachimiak, Centerfor Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.33 / 2.80
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 145.639, 145.639, 145.639, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.9

Other elements in 3fpi:

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate (pdb code 3fpi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate, PDB code: 3fpi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3fpi

Go back to Magnesium Binding Sites List in 3fpi
Magnesium binding site 1 out of 2 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate


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 Ispf Complexed with Cytidine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg167

b:0.2
occ:1.00
O3G A:CTP163 2.4 91.7 0.6
OG A:SER37 2.5 76.4 1.0
CB A:ALA35 2.8 75.0 1.0
N A:SER37 2.8 79.0 1.0
PG A:CTP163 3.1 92.1 0.6
O1G A:CTP163 3.2 90.7 0.6
O2G A:CTP163 3.3 91.7 0.6
O A:SER37 3.3 77.0 1.0
CE1 A:HIS44 3.3 69.1 1.0
CA A:SER37 3.3 77.9 1.0
CB A:SER37 3.4 77.0 1.0
N A:GLY39 3.4 67.1 1.0
C A:SER37 3.4 76.5 1.0
N A:HIS36 3.5 80.2 1.0
CA A:GLY39 3.6 63.9 1.0
C A:ALA35 3.8 79.1 1.0
CA A:ALA35 3.8 76.8 1.0
C A:HIS36 3.9 81.5 1.0
NE2 A:HIS44 4.1 68.5 1.0
CA A:HIS36 4.2 82.2 1.0
N A:ASP38 4.2 74.4 1.0
CE1 A:HIS10 4.2 71.0 1.0
NE2 A:HIS10 4.3 69.3 1.0
ND1 A:HIS44 4.3 67.3 1.0
C A:ASP38 4.6 69.7 1.0
O A:ALA35 4.6 80.9 1.0
O3B A:CTP163 4.7 90.8 0.6
CB A:HIS36 4.7 83.0 1.0
C A:GLY39 4.8 61.3 1.0
O A:HOH178 4.9 79.2 1.0
O A:HIS36 4.9 83.3 1.0
CA A:ASP38 5.0 72.3 1.0

Magnesium binding site 2 out of 2 in 3fpi

Go back to Magnesium Binding Sites List in 3fpi
Magnesium binding site 2 out of 2 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate


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 Ispf Complexed with Cytidine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg168

b:51.1
occ:0.33
O A:HOH230 3.1 77.9 1.0
CL A:CL165 3.1 30.0 0.3
CA A:GLY140 4.2 58.7 1.0
CD2 A:PHE141 4.2 54.5 1.0
N A:PHE141 4.4 58.3 1.0
CE2 A:PHE141 4.6 52.4 1.0
C A:GLY140 4.9 58.8 1.0

Reference:

Y.Kim, N.Maltseva, J.Stam, W.F.Anderson, A.Joachimiak. Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase Ispf Complexed with Cytidine Triphosphate To Be Published.
Page generated: Wed Aug 14 13:50:39 2024

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