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Magnesium in PDB 3uxm: Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation

Enzymatic activity of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation

All present enzymatic activity of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation:
2.7.4.9;

Protein crystallography data

The structure of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation, PDB code: 3uxm was solved by J.Y.Choi, M.S.Plummer, J.Starr, C.R.Desbonnet, H.H.Soutter, J.Chang, J.R.Miller, K.Dillman, A.A.Miller, W.R.Roush, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.60 / 1.95
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.877, 41.544, 117.886, 90.00, 90.02, 90.00
R / Rfree (%) 17.5 / 23.6

Other elements in 3uxm:

The structure of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation (pdb code 3uxm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation, PDB code: 3uxm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3uxm

Go back to Magnesium Binding Sites List in 3uxm
Magnesium binding site 1 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:30.9
occ:1.00
 O A:HOH259 2.0 29.4 1.0
OD2 A:ASP159 2.1 29.4 1.0
O A:HOH273 2.1 25.6 1.0
OE1 A:GLU158 2.3 17.6 1.0
O A:HOH274 2.3 30.7 1.0
CG A:ASP159 3.3 24.5 1.0
CD A:GLU158 3.3 20.3 1.0
OE2 A:GLU158 3.7 20.8 1.0
N A:ASP159 4.0 21.3 1.0
CB A:ASP159 4.1 23.5 1.0
OD1 A:ASP159 4.2 22.0 1.0
O A:HOH244 4.3 29.3 1.0
CG A:GLU158 4.6 19.9 1.0
CA A:ASP159 4.7 23.9 1.0
CA A:GLU158 4.8 22.6 1.0
CB A:GLU158 4.8 22.8 1.0
C A:GLU158 4.9 24.4 1.0

Magnesium binding site 2 out of 4 in 3uxm

Go back to Magnesium Binding Sites List in 3uxm
Magnesium binding site 2 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:41.9
occ:1.00
 O A:HOH278 2.0 23.4 1.0
O A:HOH219 2.2 23.2 1.0
OE2 A:GLU156 2.2 34.2 1.0
OE2 A:GLU12 2.3 36.1 1.0
O A:HOH270 2.6 28.0 1.0
CD A:GLU156 3.2 33.6 1.0
CD A:GLU12 3.3 34.3 1.0
CG A:GLU156 3.5 31.6 1.0
OD1 A:ASP153 3.7 31.7 1.0
O2 A:0DN800 3.7 17.6 1.0
OE1 A:GLU12 3.8 24.4 1.0
C2 A:0DN800 4.1 17.8 1.0
OE1 A:GLU156 4.3 29.6 1.0
O A:HOH275 4.4 17.7 1.0
CG A:ASP153 4.5 25.9 1.0
CG A:GLU12 4.6 33.1 1.0
OD2 A:ASP153 4.6 27.9 1.0
C1 A:0DN800 4.8 20.5 1.0
C5 A:0DN800 5.0 17.1 1.0
CB A:GLU156 5.0 25.6 1.0

Magnesium binding site 3 out of 4 in 3uxm

Go back to Magnesium Binding Sites List in 3uxm
Magnesium binding site 3 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg213

b:28.9
occ:1.00
 O C:HOH341 2.0 25.6 1.0
O C:HOH340 2.0 28.8 1.0
OD2 C:ASP159 2.1 30.2 1.0
OE1 C:GLU158 2.2 17.0 1.0
O C:HOH252 2.2 27.7 1.0
CD C:GLU158 3.3 21.8 1.0
CG C:ASP159 3.3 23.4 1.0
OE2 C:GLU158 3.6 26.4 1.0
N C:ASP159 3.9 20.7 1.0
CB C:ASP159 4.1 22.0 1.0
OD1 C:ASP159 4.2 21.1 1.0
O C:HOH224 4.2 32.5 1.0
CG C:GLU158 4.6 23.6 1.0
CA C:GLU158 4.6 24.6 1.0
CA C:ASP159 4.7 23.9 1.0
CB C:GLU158 4.8 24.6 1.0
C C:GLU158 4.8 24.6 1.0
CB C:PHE162 4.9 13.8 1.0

Magnesium binding site 4 out of 4 in 3uxm

Go back to Magnesium Binding Sites List in 3uxm
Magnesium binding site 4 out of 4 in the Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg214

b:38.1
occ:1.00
 O C:HOH277 2.0 19.9 1.0
O C:HOH256 2.1 22.1 1.0
OE2 C:GLU156 2.2 33.0 1.0
OE2 C:GLU12 2.3 32.4 1.0
CD C:GLU156 3.2 33.6 1.0
CD C:GLU12 3.4 33.9 1.0
CG C:GLU156 3.5 31.7 1.0
OD2 C:ASP153 3.8 29.2 1.0
O2 C:0DN802 3.9 17.7 1.0
OE1 C:GLU12 3.9 21.5 1.0
C2 C:0DN802 4.2 15.8 1.0
O C:HOH267 4.2 32.8 1.0
OE1 C:GLU156 4.3 35.9 1.0
O C:HOH301 4.3 34.2 1.0
O C:HOH245 4.4 15.1 1.0
CG C:GLU12 4.6 30.2 1.0
CG C:ASP153 4.6 26.4 1.0
OD1 C:ASP153 4.8 28.3 1.0
C1 C:0DN802 4.8 19.4 1.0
C5 C:0DN802 4.9 20.8 1.0
CB C:ALA146 5.0 43.0 1.0

Reference:

J.Y.Choi, M.S.Plummer, J.Starr, C.R.Desbonnet, H.Soutter, J.Chang, J.R.Miller, K.Dillman, A.A.Miller, W.R.Roush. Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit to Lead Generation. J.Med.Chem. V. 55 852 2012.
ISSN: ISSN 0022-2623
PubMed: 22243413
DOI: 10.1021/JM201349F
Page generated: Thu Aug 15 12:40:17 2024

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