Sodium in PDB 2wwh: Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT

All present enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT:
2.7.4.9;

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT, PDB code: 2wwh was solved by J.L.Whittingham, J.Carrero-Lerida, J.A.Brannigan, L.M.Ruiz-Perez, A.P.G.Silva, M.J.Fogg, A.J.Wilkinson, I.H.Gilbert, K.S.Wilson, D.Gonzalez-Pacanowska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.92 / 2.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.539, 109.539, 119.351, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 27

The binding sites of Sodium atom in the Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT (pdb code 2wwh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT, PDB code: 2wwh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:43.7 occ:1.00 O1B A:T5A211 2.2 37.3 1.0 OE2 A:GLU154 2.3 30.3 1.0 OD1 A:ASP17 2.6 23.7 1.0 PB A:T5A211 3.3 35.2 1.0 CD A:GLU154 3.4 27.6 1.0 O5E A:T5A211 3.5 27.9 1.0 O3A A:T5A211 3.5 31.9 1.0 OE1 A:GLU151 3.5 35.5 1.0 CG A:ASP17 3.6 22.8 1.0 O3B A:T5A211 3.8 34.0 1.0 CB A:ASP17 3.8 21.3 1.0 O A:HOH2063 3.9 24.1 1.0 NH1 A:ARG18 4.1 25.3 0.5 O3E A:T5A211 4.1 21.0 1.0 PA A:T5A211 4.1 26.6 1.0 CG A:GLU154 4.2 26.9 1.0 OE1 A:GLU154 4.3 25.0 1.0 C3E A:T5A211 4.4 20.8 1.0 C5E A:T5A211 4.5 22.3 1.0 CD A:GLU151 4.5 34.9 1.0 CB A:GLU151 4.5 30.6 1.0 CD A:ARG18 4.6 21.9 0.5 O2X A:T5A211 4.7 31.7 1.0 C4E A:T5A211 4.7 19.6 1.0 O1A A:T5A211 4.7 26.7 1.0 OD2 A:ASP17 4.7 21.5 1.0 CA A:ASP17 4.7 21.5 1.0 CZ A:ARG18 4.9 24.7 0.5

Sodium binding site 2 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT within 5.0Å range: probe atom residue distance (Å) B Occ A:Na213 b:23.5 occ:1.00 OD2 A:ASP98 2.4 35.2 1.0 O A:HOH2037 2.6 21.7 1.0 O2C A:T5A211 2.6 32.5 1.0 O2D A:T5A211 2.7 29.8 1.0 OG A:SER22 2.8 25.1 1.0 O A:HOH2061 2.9 23.5 1.0 CG A:ASP98 3.3 29.8 1.0 O A:HOH2036 3.4 26.9 1.0 CB A:SER22 3.5 25.2 1.0 OD1 A:ASP98 3.5 34.1 1.0 N A:SER22 3.9 24.6 1.0 PC A:T5A211 3.9 34.8 1.0 CA A:SER22 4.0 25.2 1.0 PD A:T5A211 4.0 26.8 1.0 O3C A:T5A211 4.3 31.9 1.0 CB A:ASP98 4.6 23.8 1.0 CB A:LYS21 4.7 24.4 1.0 O3A A:T5A211 4.8 31.9 1.0 C A:LYS21 4.8 24.4 1.0 O1D A:T5A211 4.8 28.1 1.0 O1C A:T5A211 4.8 34.4 1.0 O2X A:T5A211 4.9 31.7 1.0 O2A A:T5A211 4.9 26.5 1.0

Sodium binding site 3 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT within 5.0Å range: probe atom residue distance (Å) B Occ B:Na212 b:51.9 occ:1.00 O2C B:T5A211 2.2 48.0 1.0 OD2 B:ASP98 2.4 42.1 1.0 OG B:SER22 2.6 46.3 1.0 O2D B:T5A211 2.8 40.9 1.0 CG B:ASP98 3.3 37.1 1.0 O B:HOH2015 3.5 31.5 1.0 OD1 B:ASP98 3.5 40.0 1.0 PC B:T5A211 3.5 47.2 1.0 PD B:T5A211 3.8 40.0 1.0 O2X B:T5A211 3.8 48.5 1.0 N B:SER22 3.8 43.3 1.0 O3C B:T5A211 3.9 44.6 1.0 CB B:SER22 3.9 44.4 1.0 O2A B:T5A211 4.0 42.9 1.0 CA B:SER22 4.3 44.1 1.0 CB B:LYS21 4.3 42.5 1.0 NZ B:LYS21 4.3 40.2 1.0 O B:HOH2003 4.3 36.9 1.0 O1D B:T5A211 4.4 40.1 1.0 O3B B:T5A211 4.5 46.6 1.0 O1C B:T5A211 4.6 48.5 1.0 C B:LYS21 4.6 43.2 1.0 CB B:ASP98 4.6 33.3 1.0 PB B:T5A211 4.8 47.0 1.0 PA B:T5A211 4.9 42.4 1.0 CA B:LYS21 4.9 43.1 1.0

Sodium binding site 4 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT within 5.0Å range: probe atom residue distance (Å) B Occ C:Na212 b:38.5 occ:1.00 O2C C:T5A211 2.7 42.2 1.0 O2D C:T5A211 2.8 37.9 1.0 OG C:SER22 2.8 47.1 1.0 OD1 C:ASP98 2.8 44.8 1.0 O3B C:T5A211 2.9 42.4 1.0 OD2 C:ASP98 3.1 49.8 1.0 PC C:T5A211 3.2 42.7 1.0 CG C:ASP98 3.3 44.9 1.0 O3C C:T5A211 3.4 42.1 1.0 PD C:T5A211 3.5 38.5 1.0 N C:SER22 3.8 47.0 1.0 NZ C:LYS21 3.9 39.9 1.0 CB C:SER22 4.0 47.3 1.0 O1D C:T5A211 4.0 35.1 1.0 CB C:LYS21 4.0 45.8 1.0 O2A C:T5A211 4.1 36.0 1.0 CA C:SER22 4.3 47.5 1.0 PB C:T5A211 4.3 43.3 1.0 O2X C:T5A211 4.5 45.0 1.0 C C:LYS21 4.5 46.6 1.0 O3A C:T5A211 4.6 40.0 1.0 PA C:T5A211 4.6 36.8 1.0 O1C C:T5A211 4.7 41.7 1.0 O1A C:T5A211 4.7 34.8 1.0 CA C:LYS21 4.8 46.2 1.0 CB C:ASP98 4.8 41.7 1.0 O1E C:T5A211 4.9 39.5 1.0 O3D C:T5A211 5.0 39.1 1.0 CE C:LYS21 5.0 40.4 1.0 CD C:LYS21 5.0 41.3 1.0

Sodium binding site 5 out of 5 in the Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Plasmodium Falciparum Thymidylate Kinase in Complex with AP5DT within 5.0Å range: probe atom residue distance (Å) B Occ C:Na213 b:49.8 occ:1.00 OD1 C:ASP17 2.1 39.7 1.0 OE2 C:GLU154 2.4 45.5 1.0 O1B C:T5A211 2.4 43.9 1.0 O C:HOH2012 2.6 24.9 1.0 O3A C:T5A211 2.7 40.0 1.0 PB C:T5A211 2.9 43.3 1.0 CG C:ASP17 3.3 40.9 1.0 CD C:GLU154 3.5 44.9 1.0 O2X C:T5A211 3.7 45.0 1.0 O5E C:T5A211 3.8 36.0 1.0 CB C:ASP17 3.8 40.2 1.0 NE C:ARG18 3.8 37.2 0.5 PA C:T5A211 3.9 36.8 1.0 O1C C:T5A211 3.9 41.7 1.0 CG C:GLU154 4.1 42.9 1.0 OE1 C:GLU151 4.1 38.9 1.0 O3E C:T5A211 4.2 31.4 1.0 CZ C:ARG18 4.3 37.2 0.5 O3B C:T5A211 4.3 42.4 1.0 OD2 C:ASP17 4.3 38.7 1.0 CD C:ARG18 4.4 38.6 0.5 NH1 C:ARG18 4.4 35.8 0.5 CA C:ASP17 4.5 40.5 1.0 OE1 C:GLU154 4.5 45.9 1.0 C3E C:T5A211 4.6 33.4 1.0 O1A C:T5A211 4.7 34.8 1.0 CG C:ARG18 4.7 40.3 0.5 N C:ARG18 4.8 41.2 1.0 CB C:GLU151 4.8 41.8 1.0 PC C:T5A211 4.8 42.7 1.0 C4E C:T5A211 4.9 33.8 1.0 O2A C:T5A211 4.9 36.0 1.0 C5E C:T5A211 4.9 33.8 1.0

J.L.Whittingham, J.Carrero-Lerida, J.A.Brannigan, L.M.Ruiz-Perez, A.P.G.Silva, M.J.Fogg, A.J.Wilkinson, I.H.Gilbert, K.S.Wilson, D.Gonzalez-Pacanowska. Structural Basis For the Efficient Phosphorylation of Aztmp and Dgmp By Plasmodium Falciparum Type I Thymidylate Kinase. Biochem.J. V. 428 499 2010.
ISSN: ISSN 0264-6021
PubMed: 20353400
DOI: 10.1042/BJ20091880