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Magnesium in PDB 4uxj: Leishmania Major Thymidine Kinase in Complex with Dttp

Enzymatic activity of Leishmania Major Thymidine Kinase in Complex with Dttp

All present enzymatic activity of Leishmania Major Thymidine Kinase in Complex with Dttp:
2.7.1.21;

Protein crystallography data

The structure of Leishmania Major Thymidine Kinase in Complex with Dttp, PDB code: 4uxj was solved by J.Timm, C.Bosch-Navarrete, E.Recio, J.E.Nettleship, H.Rada, D.Gonzalez-Pacanowska, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 108.69 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.600, 61.630, 110.090, 81.07, 85.80, 74.94
R / Rfree (%) 26.03 / 27.837

Other elements in 4uxj:

The structure of Leishmania Major Thymidine Kinase in Complex with Dttp also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Leishmania Major Thymidine Kinase in Complex with Dttp (pdb code 4uxj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Leishmania Major Thymidine Kinase in Complex with Dttp, PDB code: 4uxj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4uxj

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Magnesium binding site 1 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1185

b:34.3
occ:1.00
 OG1 A:THR18 2.2 43.9 1.0
O2B A:TTP1184 2.5 40.5 1.0
O2A A:TTP1184 2.5 37.8 1.0
O2G A:TTP1184 2.5 26.5 1.0
CB A:THR18 3.1 37.4 1.0
PG A:TTP1184 3.8 33.1 1.0
PB A:TTP1184 3.8 36.9 1.0
CG2 A:THR18 3.8 37.8 1.0
PA A:TTP1184 3.9 39.4 1.0
OE2 A:GLU85 3.9 51.7 1.0
O3B A:TTP1184 4.1 35.6 1.0
OD2 A:ASP84 4.2 40.7 1.0
O3A A:TTP1184 4.3 36.1 1.0
O1G A:TTP1184 4.4 28.6 1.0
CA A:THR18 4.4 33.8 1.0
N A:THR18 4.5 32.5 1.0
OD1 A:ASP84 4.7 39.9 1.0
O5' A:TTP1184 4.7 46.7 1.0
CG A:ASP84 4.9 40.5 1.0

Magnesium binding site 2 out of 8 in 4uxj

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Magnesium binding site 2 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1182

b:19.5
occ:1.00
 OG1 B:THR18 2.2 32.6 1.0
O1B B:TTP1181 2.2 42.9 1.0
O2A B:TTP1181 2.6 42.1 1.0
O3G B:TTP1181 2.6 63.0 1.0
CB B:THR18 3.1 30.2 1.0
PG B:TTP1181 3.5 64.8 1.0
PB B:TTP1181 3.5 41.2 1.0
O1G B:TTP1181 3.7 62.2 1.0
O3B B:TTP1181 3.8 53.8 1.0
CG2 B:THR18 3.9 30.5 1.0
PA B:TTP1181 3.9 45.0 1.0
OE1 B:GLU85 4.1 36.8 1.0
O3A B:TTP1181 4.2 39.6 1.0
OD2 B:ASP84 4.2 30.9 1.0
CA B:THR18 4.4 28.3 1.0
N B:THR18 4.5 28.0 1.0
OD1 B:ASP84 4.6 30.3 1.0
O5' B:TTP1181 4.6 42.3 1.0
O2B B:TTP1181 4.8 41.0 1.0
CG B:ASP84 4.9 29.8 1.0
CD B:GLU85 4.9 36.7 1.0
O2G B:TTP1181 5.0 55.2 1.0

Magnesium binding site 3 out of 8 in 4uxj

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Magnesium binding site 3 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1182

b:8.7
occ:1.00
 O2B C:TTP1181 2.0 13.7 1.0
O2A C:TTP1181 2.2 15.4 1.0
OG1 C:THR18 2.2 16.6 1.0
O2G C:TTP1181 2.5 15.3 1.0
CB C:THR18 3.2 17.1 1.0
PB C:TTP1181 3.3 14.8 1.0
PA C:TTP1181 3.5 15.4 1.0
PG C:TTP1181 3.6 15.3 1.0
O3B C:TTP1181 3.7 15.6 1.0
O C:HOH2012 3.8 26.2 1.0
O3A C:TTP1181 3.9 15.2 1.0
CG2 C:THR18 4.0 17.6 1.0
OD2 C:ASP84 4.4 37.2 1.0
CA C:THR18 4.4 17.4 1.0
N C:THR18 4.4 18.1 1.0
O1G C:TTP1181 4.4 13.9 1.0
O5' C:TTP1181 4.4 17.1 1.0
OD1 C:ASP84 4.6 42.5 1.0
O1B C:TTP1181 4.6 13.6 1.0
O1A C:TTP1181 4.6 16.6 1.0
O3G C:TTP1181 4.8 14.8 1.0
CG C:ASP84 4.9 37.4 1.0

Magnesium binding site 4 out of 8 in 4uxj

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Magnesium binding site 4 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1182

b:40.3
occ:1.00
 O1A D:TTP1181 2.0 58.4 1.0
OG1 D:THR18 2.2 51.0 1.0
O1G D:TTP1181 2.5 39.8 1.0
O2B D:TTP1181 2.6 38.3 1.0
O2G D:TTP1181 2.7 39.3 1.0
PG D:TTP1181 3.0 37.6 1.0
CB D:THR18 3.2 47.5 1.0
PA D:TTP1181 3.3 62.7 1.0
PB D:TTP1181 3.5 48.2 1.0
O3B D:TTP1181 3.6 43.8 1.0
O3A D:TTP1181 3.7 55.5 1.0
O2A D:TTP1181 4.2 75.6 1.0
N D:THR18 4.2 40.4 1.0
CG2 D:THR18 4.2 50.9 1.0
CA D:THR18 4.3 43.3 1.0
O5' D:TTP1181 4.4 59.5 1.0
O3G D:TTP1181 4.5 36.8 1.0
OD2 D:ASP84 4.5 58.5 1.0
OD1 D:ASP84 4.6 58.5 1.0
OE1 D:GLU85 4.7 78.7 1.0
O1B D:TTP1181 5.0 43.1 1.0

Magnesium binding site 5 out of 8 in 4uxj

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Magnesium binding site 5 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1182

b:17.2
occ:1.00
 O2G E:TTP1181 2.0 51.5 1.0
OG1 E:THR18 2.2 37.1 1.0
O2A E:TTP1181 2.3 42.4 1.0
O2B E:TTP1181 2.7 28.8 1.0
PG E:TTP1181 3.2 46.9 1.0
CB E:THR18 3.2 36.1 1.0
PB E:TTP1181 3.5 32.5 1.0
PA E:TTP1181 3.5 35.8 1.0
O3B E:TTP1181 3.5 38.7 1.0
O3A E:TTP1181 3.6 31.1 1.0
O1G E:TTP1181 3.7 41.0 1.0
CG2 E:THR18 4.1 37.0 1.0
N E:THR18 4.3 34.0 1.0
CA E:THR18 4.3 34.8 1.0
O3G E:TTP1181 4.5 46.7 1.0
O1A E:TTP1181 4.5 37.8 1.0
OD2 E:ASP84 4.5 35.9 1.0
O5' E:TTP1181 4.5 34.6 1.0
OD1 E:ASP84 4.7 36.0 1.0
OE1 E:GLU85 4.8 43.8 1.0
O1B E:TTP1181 5.0 31.8 1.0

Magnesium binding site 6 out of 8 in 4uxj

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Magnesium binding site 6 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1184

b:26.8
occ:1.00
 O2G F:TTP1183 1.6 38.1 1.0
O1A F:TTP1183 1.7 26.2 1.0
OG1 F:THR18 2.2 35.5 1.0
O3A F:TTP1183 2.9 30.6 1.0
PA F:TTP1183 2.9 28.5 1.0
PG F:TTP1183 3.0 37.0 1.0
O2B F:TTP1183 3.1 32.0 1.0
CB F:THR18 3.4 31.5 1.0
O3G F:TTP1183 3.5 33.9 1.0
PB F:TTP1183 3.5 31.2 1.0
O3B F:TTP1183 3.8 32.1 1.0
O2A F:TTP1183 3.8 32.1 1.0
N F:THR18 3.8 29.1 1.0
O5' F:TTP1183 4.0 28.1 1.0
O1G F:TTP1183 4.1 39.7 1.0
OE2 F:GLU85 4.1 40.8 1.0
CA F:THR18 4.2 29.5 1.0
OD1 F:ASP84 4.4 37.3 1.0
CG2 F:THR18 4.5 31.9 1.0
NZ F:LYS17 4.5 29.5 1.0
OD2 F:ASP84 4.7 36.8 1.0
CB F:LYS17 4.8 28.1 1.0
CE F:LYS17 4.8 29.1 1.0
O1B F:TTP1183 4.9 31.2 1.0
OG F:SER109 5.0 34.4 1.0
C F:LYS17 5.0 28.1 1.0
CG F:ASP84 5.0 36.2 1.0

Magnesium binding site 7 out of 8 in 4uxj

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Magnesium binding site 7 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1182

b:10.2
occ:1.00
 O2A G:TTP1181 1.9 16.5 1.0
OG1 G:THR18 2.2 24.5 1.0
O2G G:TTP1181 2.3 19.9 1.0
O2B G:TTP1181 2.4 12.5 1.0
PA G:TTP1181 3.2 16.4 1.0
CB G:THR18 3.3 23.9 1.0
PB G:TTP1181 3.4 13.7 1.0
PG G:TTP1181 3.5 19.7 1.0
O3A G:TTP1181 3.6 14.8 1.0
O3B G:TTP1181 3.7 17.4 1.0
O1A G:TTP1181 4.1 18.5 1.0
CG2 G:THR18 4.1 24.9 1.0
O1G G:TTP1181 4.1 18.8 1.0
OD2 G:ASP84 4.3 49.1 1.0
O5' G:TTP1181 4.4 18.9 1.0
N G:THR18 4.4 22.6 1.0
CA G:THR18 4.4 23.3 1.0
OD1 G:ASP84 4.5 50.6 1.0
OE1 G:GLU85 4.5 44.8 1.0
O3G G:TTP1181 4.7 19.6 1.0
O1B G:TTP1181 4.8 12.5 1.0
CG G:ASP84 4.9 46.8 1.0
CD G:GLU85 4.9 42.7 1.0

Magnesium binding site 8 out of 8 in 4uxj

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Magnesium binding site 8 out of 8 in the Leishmania Major Thymidine Kinase in Complex with Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Leishmania Major Thymidine Kinase in Complex with Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1180

b:37.4
occ:1.00
 O2A H:TTP1179 1.7 60.6 1.0
OG1 H:THR18 2.2 58.9 1.0
O2G H:TTP1179 2.2 50.0 1.0
O2B H:TTP1179 2.8 41.1 1.0
PA H:TTP1179 3.1 60.5 1.0
PG H:TTP1179 3.2 57.8 1.0
CB H:THR18 3.3 57.9 1.0
O1G H:TTP1179 3.4 61.3 1.0
O3B H:TTP1179 3.7 56.6 1.0
PB H:TTP1179 3.7 48.8 1.0
O1A H:TTP1179 3.9 68.8 1.0
O3A H:TTP1179 3.9 54.0 1.0
O5' H:TTP1179 4.2 63.1 1.0
N H:THR18 4.2 52.0 1.0
CG2 H:THR18 4.2 60.8 1.0
CA H:THR18 4.3 55.1 1.0
OD2 H:ASP84 4.4 72.0 1.0
OD1 H:ASP84 4.4 63.0 1.0
O3G H:TTP1179 4.6 50.9 1.0
CG H:ASP84 4.9 66.9 1.0

Reference:

J.Timm, C.Bosch-Navarrete, E.Recio, J.E.Nettleship, H.Rada, D.Gonzalez-Pacanowska, K.S.Wilson. Structural and Kinetic Characterization of Thymidine Kinase From Leishmania Major. Plos Negl Trop Dis V. 9 3781 2015.
ISSN: ISSN 1935-2727
PubMed: 25978379
DOI: 10.1371/JOURNAL.PNTD.0003781
Page generated: Tue Aug 20 05:00:49 2024

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