Atomistry » Chlorine » PDB 2yjb-2yzr » 2yof
Atomistry »
  Chlorine »
    PDB 2yjb-2yzr »
      2yof »

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

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

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

Protein crystallography data

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor, PDB code: 2yof 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) 94.95 / 1.82
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.639, 109.639, 121.892, 90.00, 90.00, 120.00
R / Rfree (%) 18.856 / 23.086

Other elements in 2yof:

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

Fluorine (F) 15 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor (pdb code 2yof). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor, PDB code: 2yof:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 2yof

Go back to Chlorine Binding Sites List in 2yof
Chlorine binding site 1 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-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-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:58.0
occ:0.50
 CL A:74W211 0.0 58.0 0.5
CL A:74W211 1.7 35.3 0.5
CAW A:74W211 1.7 57.5 0.5
FAG A:74W211 1.9 33.3 0.5
CAW A:74W211 2.0 31.9 0.5
CBE A:74W211 2.2 32.5 0.5
CAX A:74W211 2.3 32.0 0.5
FAH A:74W211 2.3 32.9 0.5
FAG A:74W211 2.7 59.5 0.5
CAX A:74W211 2.7 57.9 0.5
CAK A:74W211 2.7 56.9 0.5
NH2 A:ARG18 2.8 38.8 0.5
CBE A:74W211 3.0 59.0 0.5
FAH A:74W211 3.2 59.8 0.5
CAK A:74W211 3.2 31.3 0.5
CG A:GLU154 3.5 40.5 1.0
CAL A:74W211 3.5 29.9 0.5
FAF A:74W211 3.6 33.0 0.5
CD A:GLU154 3.8 41.8 0.5
OE2 A:GLU154 3.8 42.4 0.5
CZ A:ARG18 3.9 38.9 0.5
CAJ A:74W211 4.0 55.7 0.5
CAL A:74W211 4.0 56.1 0.5
CB A:GLU154 4.2 37.3 1.0
CAJ A:74W211 4.2 30.1 0.5
OE1 A:GLU150 4.3 50.2 1.0
FAF A:74W211 4.3 59.2 0.5
NH1 A:ARG18 4.3 38.9 0.5
CAV A:74W211 4.4 28.7 0.5
CD A:GLU150 4.4 48.4 1.0
OE1 A:GLU154 4.5 42.5 0.5
OE2 A:GLU150 4.5 49.7 1.0
CAV A:74W211 4.6 54.7 0.5
CB A:GLU151 4.7 35.8 1.0
CA A:GLU154 4.7 37.5 1.0
NE A:ARG18 4.9 39.6 0.5
N A:GLU151 4.9 37.7 1.0

Chlorine binding site 2 out of 5 in 2yof

Go back to Chlorine Binding Sites List in 2yof
Chlorine binding site 2 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-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-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:35.3
occ:0.50
 CL A:74W211 0.0 35.3 0.5
CL A:74W211 1.7 58.0 0.5
CAW A:74W211 1.8 31.9 0.5
CAW A:74W211 2.3 57.5 0.5
FAH A:74W211 2.6 32.9 0.5
CAX A:74W211 2.7 32.0 0.5
CAK A:74W211 2.8 31.3 0.5
CAK A:74W211 2.9 56.9 0.5
CBE A:74W211 3.1 32.5 0.5
CAX A:74W211 3.2 57.9 0.5
FAH A:74W211 3.2 59.8 0.5
CD A:GLU150 3.3 48.4 1.0
FAG A:74W211 3.4 33.3 0.5
N A:GLU151 3.5 37.7 1.0
CD A:GLU154 3.5 41.8 0.5
OE1 A:GLU150 3.5 50.2 1.0
CG A:GLU150 3.5 44.4 1.0
CB A:GLU151 3.6 35.8 1.0
OE2 A:GLU150 3.6 49.7 1.0
CBE A:74W211 3.6 59.0 0.5
CB A:GLU150 3.6 41.4 1.0
OE2 A:GLU154 3.7 42.4 0.5
FAG A:74W211 3.7 59.5 0.5
CG A:GLU154 3.8 40.5 1.0
OE1 A:GLU154 3.8 42.5 0.5
CG A:GLU151 4.0 35.2 1.0
CAL A:74W211 4.0 29.9 0.5
CAJ A:74W211 4.1 30.1 0.5
CAJ A:74W211 4.1 55.7 0.5
CA A:GLU151 4.1 35.9 1.0
C A:GLU150 4.1 39.8 1.0
NH2 A:ARG18 4.2 38.8 0.5
CB A:GLU154 4.2 37.3 1.0
CAL A:74W211 4.3 56.1 0.5
FAF A:74W211 4.3 33.0 0.5
CA A:GLU150 4.4 41.0 1.0
CAV A:74W211 4.6 28.7 0.5
CD A:GLU151 4.6 35.9 1.0
CAV A:74W211 4.7 54.7 0.5
OE1 A:GLU151 4.8 34.4 1.0
O A:GLU151 4.8 34.8 1.0
FAF A:74W211 4.9 59.2 0.5
O A:GLU150 4.9 40.2 1.0
C A:GLU151 4.9 35.0 1.0
N A:GLU150 5.0 41.4 1.0

Chlorine binding site 3 out of 5 in 2yof

Go back to Chlorine Binding Sites List in 2yof
Chlorine binding site 3 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl211

b:47.1
occ:0.70
 CL B:74W211 0.0 47.1 0.7
CAW B:74W211 1.7 42.8 0.7
CAX B:74W211 2.7 41.5 0.7
CAK B:74W211 2.8 41.0 0.7
FAH B:74W211 2.8 41.5 0.7
FAG B:74W211 2.9 42.6 0.7
CBE B:74W211 2.9 42.1 0.7
O B:HOH2186 3.4 53.4 1.0
N B:GLU150 3.5 38.5 1.0
N B:GLU151 3.7 32.2 1.0
CB B:GLU151 3.7 29.9 0.5
CG B:GLU151 3.9 31.0 0.5
CB B:GLU151 3.9 31.0 0.5
CAL B:74W211 4.0 39.7 0.7
CB B:GLU154 4.0 31.6 1.0
OE1 B:GLU154 4.0 43.0 1.0
CAJ B:74W211 4.1 40.1 0.7
FAF B:74W211 4.3 42.2 0.7
CG B:GLU151 4.3 27.7 0.5
CA B:GLU151 4.3 30.6 0.5
C B:GLU150 4.3 35.3 1.0
CA B:GLU151 4.3 31.2 0.5
CA B:GLU150 4.4 37.7 1.0
CAV B:74W211 4.6 39.4 0.7
CD B:GLU151 4.7 25.3 0.5
OE1 B:GLU151 4.8 21.2 0.5
CD B:GLU154 4.8 40.9 1.0
O B:GLU151 4.8 30.3 1.0
CA B:GLU154 5.0 31.1 1.0

Chlorine binding site 4 out of 5 in 2yof

Go back to Chlorine Binding Sites List in 2yof
Chlorine binding site 4 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl211

b:46.3
occ:0.50
 CL C:74W211 0.0 46.3 0.5
CAW C:74W211 1.7 42.8 0.5
CAX C:74W211 2.7 42.6 0.5
CAK C:74W211 2.7 41.3 0.5
FAH C:74W211 2.8 63.2 0.5
FAF C:74W211 2.8 43.9 0.5
FAH C:74W211 2.9 44.2 0.5
CBE C:74W211 3.0 43.5 0.5
CBE C:74W211 3.9 62.7 0.5
CAJ C:74W211 4.0 39.6 0.5
CAL C:74W211 4.0 40.0 0.5
CAX C:74W211 4.0 62.2 0.5
FAG C:74W211 4.3 43.6 0.5
CAW C:74W211 4.3 62.2 0.5
CAV C:74W211 4.5 37.7 0.5
CAL C:74W211 4.5 60.7 0.5
CL C:74W211 4.6 63.5 0.5
FAG C:74W211 4.6 63.0 0.5
FAF C:74W211 4.8 62.7 0.5

Chlorine binding site 5 out of 5 in 2yof

Go back to Chlorine Binding Sites List in 2yof
Chlorine binding site 5 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl211

b:63.5
occ:0.50
 CL C:74W211 0.0 63.5 0.5
CAW C:74W211 1.7 62.2 0.5
FAG C:74W211 2.6 63.0 0.5
CAK C:74W211 2.7 61.5 0.5
CAX C:74W211 2.7 62.2 0.5
CBE C:74W211 3.1 62.7 0.5
FAH C:74W211 3.6 63.2 0.5
CB C:SER22 3.6 34.3 1.0
O C:HOH2017 3.8 47.8 1.0
CAJ C:74W211 4.0 60.4 0.5
CAL C:74W211 4.0 60.7 0.5
OG C:SER22 4.1 38.0 1.0
FAF C:74W211 4.1 43.9 0.5
FAF C:74W211 4.3 62.7 0.5
OD2 C:ASP98 4.5 31.3 1.0
CAW C:74W211 4.5 42.8 0.5
CAV C:74W211 4.5 59.4 0.5
CL C:74W211 4.6 46.3 0.5
CAX C:74W211 4.7 42.6 0.5
CAK C:74W211 4.8 41.3 0.5
CA C:SER22 5.0 34.0 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 15:14:20 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy