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Sodium in PDB 2wwg: Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp

Enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp

All present enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp:
2.7.4.9;

Protein crystallography data

The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp, PDB code: 2wwg was solved by J.L.Whittingham, J.Carrero-Lerida, J.A.Brannigan, L.M.Ruiz- Perez, A.P.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) 95.90 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.741, 110.741, 119.361, 90.00, 90.00, 120.00
R / Rfree (%) 19.005 / 25.759

Sodium Binding Sites:

The binding sites of Sodium atom in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp (pdb code 2wwg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp, PDB code: 2wwg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2wwg

Go back to Sodium Binding Sites List in 2wwg
Sodium binding site 1 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp


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 Dgmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na213

b:46.0
occ:1.00
 O A:HOH2081 2.4 35.3 1.0
OG A:SER22 2.4 36.0 1.0
O A:HOH2012 2.6 40.7 1.0
O2B A:ADP212 2.7 31.9 1.0
O A:HOH2014 2.9 40.0 1.0
CB A:SER22 3.7 31.1 1.0
O A:HOH2013 3.7 61.4 1.0
OD2 A:ASP98 3.7 48.5 1.0
O1B A:ADP212 3.9 34.8 1.0
PB A:ADP212 3.9 30.4 1.0
O A:HOH2022 3.9 33.8 1.0
OP1 A:DGP211 4.1 38.9 1.0
N A:SER22 4.2 29.4 1.0
CA A:SER22 4.3 31.7 1.0
CG A:ASP98 4.4 40.6 1.0
O A:HOH2008 4.5 32.7 1.0
CB A:ASP98 4.5 34.7 1.0
OP2 A:DGP211 4.5 37.4 1.0
O A:HOH2004 4.6 51.9 1.0
NZ A:LYS21 4.6 25.5 1.0
O3B A:ADP212 4.7 32.0 1.0
OP3 A:DGP211 4.7 36.1 1.0
P A:DGP211 4.8 38.2 1.0
CB A:LYS21 4.8 28.0 1.0
O1A A:ADP212 4.9 32.7 1.0

Sodium binding site 2 out of 6 in 2wwg

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Sodium binding site 2 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp


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 Dgmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na214

b:59.8
occ:1.00
 O A:HOH2062 2.2 57.0 1.0
OD1 A:ASP17 2.5 30.7 1.0
OP3 A:DGP211 2.6 36.1 1.0
O A:HOH2010 2.9 47.3 1.0
OE2 A:GLU154 3.1 45.4 1.0
O A:HOH2008 3.2 32.7 1.0
P A:DGP211 3.5 38.2 1.0
CG A:ASP17 3.5 32.7 1.0
CB A:ASP17 3.7 31.7 1.0
NH1 A:ARG18 3.8 55.1 1.0
OP2 A:DGP211 3.8 37.4 1.0
C5' A:DGP211 4.0 33.7 1.0
CD A:GLU154 4.2 39.1 1.0
O5' A:DGP211 4.2 37.2 1.0
O3' A:DGP211 4.2 22.1 1.0
C3' A:DGP211 4.2 27.3 1.0
CA A:ASP17 4.2 31.7 1.0
O A:HOH2081 4.5 35.3 1.0
O A:HOH2063 4.5 42.2 1.0
NH2 A:ARG99 4.5 21.0 1.0
C4' A:DGP211 4.6 30.2 1.0
OD2 A:ASP17 4.6 32.4 1.0
N A:ARG18 4.7 32.4 1.0
O1B A:ADP212 4.7 34.8 1.0
OE1 A:GLU151 4.7 45.1 1.0
CG A:GLU154 4.8 35.2 1.0
CD A:ARG18 4.8 43.0 1.0
OP1 A:DGP211 4.9 38.9 1.0
CZ A:ARG18 4.9 51.6 1.0
C A:ASP17 5.0 32.7 1.0

Sodium binding site 3 out of 6 in 2wwg

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Sodium binding site 3 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp


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 Dgmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na213

b:47.9
occ:1.00
 O3B B:ADP212 2.2 43.9 1.0
OG B:SER22 2.3 45.6 1.0
O B:HOH2009 2.4 42.4 1.0
OD2 B:ASP98 2.4 43.1 1.0
O B:HOH2010 3.1 59.8 1.0
CB B:SER22 3.5 44.3 1.0
CG B:ASP98 3.5 41.1 1.0
PB B:ADP212 3.5 44.4 1.0
N B:SER22 3.6 43.0 1.0
OD1 B:ASP98 3.8 47.7 1.0
O2B B:ADP212 3.9 45.5 1.0
CA B:SER22 3.9 43.8 1.0
CB B:LYS21 4.3 41.8 1.0
NZ B:LYS21 4.4 38.5 1.0
O1B B:ADP212 4.4 44.0 1.0
O B:HOH2008 4.4 41.2 1.0
C B:LYS21 4.5 42.8 1.0
OP2 B:DGP211 4.5 38.0 1.0
O1A B:ADP212 4.6 48.3 1.0
OP3 B:DGP211 4.7 44.6 1.0
O3A B:ADP212 4.8 48.7 1.0
CB B:ASP98 4.8 35.4 1.0
CA B:LYS21 4.8 42.3 1.0

Sodium binding site 4 out of 6 in 2wwg

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Sodium binding site 4 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp


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 Dgmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na214

b:66.3
occ:1.00
 O B:HOH2005 2.4 57.2 1.0
OD1 B:ASP17 2.5 43.3 1.0
OP3 B:DGP211 2.5 44.6 1.0
O B:HOH2008 3.0 41.2 1.0
O B:HOH2007 3.0 54.6 1.0
P B:DGP211 3.3 39.8 1.0
O5' B:DGP211 3.4 37.4 1.0
CG B:ASP17 3.4 43.7 1.0
CB B:ASP17 3.8 40.6 1.0
OE2 B:GLU154 3.8 55.5 1.0
OP2 B:DGP211 3.9 38.0 1.0
C3' B:DGP211 4.1 31.3 1.0
O3' B:DGP211 4.2 32.1 1.0
CA B:ASP17 4.2 40.5 1.0
O2B B:ADP212 4.4 45.5 1.0
CD B:GLU154 4.5 53.2 1.0
C5' B:DGP211 4.5 31.3 1.0
NH2 B:ARG18 4.5 62.6 1.0
OD2 B:ASP17 4.6 48.0 1.0
CZ B:ARG18 4.6 63.3 1.0
OE1 B:GLU151 4.7 51.8 1.0
C4' B:DGP211 4.7 30.5 1.0
NE B:ARG18 4.7 61.8 1.0
OP1 B:DGP211 4.7 40.7 1.0
NH2 B:ARG99 4.8 28.4 1.0
N B:ARG18 4.8 42.0 1.0
CG B:GLU154 4.9 52.4 1.0

Sodium binding site 5 out of 6 in 2wwg

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Sodium binding site 5 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp


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 Dgmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na213

b:69.0
occ:1.00
 O1B C:ADP212 2.5 40.0 1.0
OG C:SER22 2.8 51.2 1.0
OP3 C:DGP211 3.5 48.9 1.0
PB C:ADP212 3.6 45.1 1.0
OD2 C:ASP98 3.6 59.1 1.0
O3B C:ADP212 3.7 44.9 1.0
OP2 C:DGP211 4.0 49.0 1.0
O C:HOH2005 4.0 49.3 1.0
P C:DGP211 4.1 50.1 1.0
CB C:SER22 4.2 49.5 1.0
O2B C:ADP212 4.3 41.7 1.0
CG C:ASP98 4.3 52.8 1.0
O C:HOH2003 4.3 43.0 1.0
OP1 C:DGP211 4.3 49.1 1.0
OD1 C:ASP98 4.3 58.7 1.0
O1A C:ADP212 4.4 51.5 1.0
N C:SER22 4.6 49.4 1.0
NZ C:LYS21 4.8 37.3 1.0
CA C:SER22 4.9 49.6 1.0
CB C:LYS21 5.0 49.8 1.0

Sodium binding site 6 out of 6 in 2wwg

Go back to Sodium Binding Sites List in 2wwg
Sodium binding site 6 out of 6 in the Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Plasmodium Falciparum Thymidylate Kinase in Complex with Dgmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na214

b:55.1
occ:1.00
 OD2 C:ASP17 2.2 41.2 1.0
OE2 C:GLU154 2.7 49.6 1.0
OP3 C:DGP211 3.0 48.9 1.0
CG C:ASP17 3.4 47.5 1.0
O5' C:DGP211 3.5 48.3 1.0
P C:DGP211 3.7 50.1 1.0
O C:HOH2003 3.8 43.0 1.0
CD C:GLU154 3.8 47.3 1.0
CB C:ASP17 3.9 46.2 1.0
O3' C:DGP211 4.1 49.5 1.0
OE1 C:GLU151 4.1 50.1 1.0
NE C:ARG18 4.3 59.1 1.0
OD1 C:ASP17 4.4 49.7 1.0
C3' C:DGP211 4.4 48.7 1.0
CG C:GLU154 4.5 44.3 1.0
OP2 C:DGP211 4.5 49.0 1.0
CA C:ASP17 4.5 46.5 1.0
O C:HOH2026 4.6 47.9 1.0
C5' C:DGP211 4.7 43.1 1.0
OE1 C:GLU154 4.7 45.3 1.0
C4' C:DGP211 4.7 46.0 1.0
CZ C:ARG18 4.7 63.6 1.0
N C:ARG18 4.8 47.6 1.0
NH2 C:ARG18 4.8 65.6 1.0
CD C:ARG18 4.9 57.7 1.0

Reference:

J.L.Whittingham, J.Carrero-Lerida, J.A.Brannigan, L.M.Ruiz-Perez, A.P.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
Page generated: Mon Oct 7 04:57:50 2024

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