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Chlorine in PDB 2yog: Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor

Enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor

All present enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor:
2.7.4.9;

Protein crystallography data

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor, PDB code: 2yog was solved by C.Huaqing, J.Carrero-Lerida, A.P.G.Silva, J.L.Whittingham, J.A.Brannigan, L.M.Ruiz-Perez, K.D.Read, K.S.Wilson, D.Gonzalez-Pacanowska, I.H.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.37 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.060, 58.790, 71.710, 90.00, 95.78, 90.00
R / Rfree (%) 18.233 / 23.262

Other elements in 2yog:

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor (pdb code 2yog). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor, PDB code: 2yog:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 2yog

Go back to Chlorine Binding Sites List in 2yog
Chlorine binding site 1 out of 2 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:44.0
occ:0.50
CLA A:74X211 0.0 44.0 0.5
CAW A:74X211 1.7 41.5 0.5
CAK A:74X211 2.7 40.9 0.5
CAX A:74X211 2.7 41.1 0.5
FAF A:74X211 3.0 42.0 0.5
CBE A:74X211 3.2 41.5 0.5
FAG A:74X211 3.3 42.1 0.5
CAJ A:74X211 4.0 39.6 0.5
CAL A:74X211 4.0 39.4 0.5
O A:HOH2081 4.4 40.3 1.0
FAH A:74X211 4.5 42.3 0.5
O A:LEU59 4.5 23.9 1.0
CAV A:74X211 4.5 38.4 1.0
CG A:LYS60 4.5 26.8 0.5
CG A:LYS60 4.8 26.7 0.5
CA A:LYS60 5.0 25.9 0.5
CA A:LYS60 5.0 25.9 0.5

Chlorine binding site 2 out of 2 in 2yog

Go back to Chlorine Binding Sites List in 2yog
Chlorine binding site 2 out of 2 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Alpha-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl211

b:34.2
occ:1.00
CLA B:74X211 0.0 34.2 1.0
CAW B:74X211 1.7 28.9 1.0
CAK B:74X211 2.7 30.7 1.0
CAX B:74X211 2.7 25.8 1.0
FAG B:74X211 3.0 23.5 1.0
FAH B:74X211 3.1 26.9 1.0
CBE B:74X211 3.1 24.9 1.0
O B:HOH2022 3.4 34.9 1.0
CG B:LYS60 3.7 18.5 1.0
O B:LEU59 4.0 16.2 1.0
O B:HOH2069 4.0 27.6 1.0
CAL B:74X211 4.0 23.4 1.0
CAJ B:74X211 4.0 28.6 1.0
CA B:LYS60 4.1 17.5 1.0
C B:LEU59 4.3 15.4 1.0
N B:LYS60 4.4 15.9 1.0
O B:HOH2071 4.4 44.7 1.0
FAF B:74X211 4.4 25.5 1.0
CB B:LYS60 4.5 16.8 1.0
CAV B:74X211 4.5 25.9 1.0
CD B:LYS60 4.7 21.6 1.0
CE B:LYS60 4.9 24.5 1.0

Reference:

H.Cui, J.Carrero-Lerida, A.P.G.Silva, J.L.Whittingham, J.A.Brannigan, L.M.Ruiz-Perez, K.D.Read, K.S.Wilson, D.Gonzalez-Pacanowska, I.H.Gilbert. Synthesis and Evaluation of Alpha-Thymidine Analogues As Novel Antimalarials. J.Med.Chem. V. 55 10948 2012.
ISSN: ISSN 0022-2623
PubMed: 23240776
DOI: 10.1021/JM301328H
Page generated: Sat Jul 20 15:14:49 2024

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