Atomistry » Zinc » PDB 4ura-4uxy » 4uxj
Atomistry »
  Zinc »
    PDB 4ura-4uxy »
      4uxj »

Zinc 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:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Leishmania Major Thymidine Kinase in Complex with Dttp, PDB code: 4uxj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1183

b:45.7
occ:1.00
 SG A:CYS176 2.3 56.4 1.0
SG A:CYS140 2.3 55.9 1.0
SG A:CYS143 2.3 63.7 1.0
SG A:CYS173 2.3 57.6 1.0
CB A:CYS140 3.2 54.6 1.0
CB A:CYS143 3.2 65.7 1.0
CB A:CYS176 3.3 56.5 1.0
CB A:CYS173 3.5 52.4 1.0
N A:CYS143 3.8 59.6 1.0
N A:CYS173 4.0 48.7 1.0
CA A:CYS143 4.1 62.8 1.0
CA A:CYS173 4.3 49.4 1.0
CA A:CYS176 4.5 57.2 1.0
N A:CYS176 4.5 56.4 1.0
CB A:GLN146 4.7 54.1 1.0
CA A:CYS140 4.7 50.3 1.0
OE2 A:GLU175 4.8 61.1 1.0
CB A:MET142 4.8 61.6 1.0
C A:CYS143 4.8 62.4 1.0
C A:MET142 4.9 60.6 1.0
C A:CYS173 5.0 48.3 1.0

Zinc binding site 2 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1180

b:57.2
occ:1.00
 SG B:CYS143 2.3 72.8 1.0
SG B:CYS176 2.3 77.2 1.0
SG B:CYS140 2.3 89.9 1.0
SG B:CYS173 2.4 75.2 1.0
CB B:CYS143 3.2 77.9 1.0
CB B:CYS140 3.2 79.1 1.0
CB B:CYS176 3.4 73.5 1.0
CB B:CYS173 3.5 67.0 1.0
N B:CYS143 3.7 75.6 1.0
CA B:CYS143 4.0 77.5 1.0
N B:CYS173 4.0 61.6 1.0
OE1 B:GLN146 4.3 88.7 1.0
CA B:CYS173 4.4 62.6 1.0
CA B:CYS176 4.5 70.8 1.0
N B:CYS176 4.5 67.4 1.0
CB B:GLN146 4.6 83.1 1.0
CA B:CYS140 4.7 75.2 1.0
C B:CYS143 4.8 76.0 1.0
CB B:MET142 4.8 78.2 1.0
C B:MET142 4.9 75.8 1.0
N B:HIS144 5.0 76.2 1.0

Zinc binding site 3 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1180

b:42.3
occ:1.00
 SG C:CYS143 2.3 62.2 1.0
SG C:CYS173 2.3 54.4 1.0
SG C:CYS176 2.4 56.0 1.0
SG C:CYS140 2.4 56.0 1.0
CB C:CYS140 3.2 51.5 1.0
CB C:CYS143 3.3 63.1 1.0
CB C:CYS176 3.4 53.6 1.0
CB C:CYS173 3.4 51.6 1.0
N C:CYS143 3.8 58.1 1.0
N C:CYS173 4.0 46.5 1.0
CA C:CYS143 4.1 60.3 1.0
OE1 C:GLN146 4.3 60.1 1.0
CA C:CYS173 4.3 48.0 1.0
N C:CYS176 4.5 56.3 1.0
CA C:CYS176 4.5 54.5 1.0
CB C:GLN146 4.5 52.8 1.0
CA C:CYS140 4.7 47.3 1.0
CB C:MET142 4.8 53.4 1.0
C C:CYS143 4.9 59.7 1.0
C C:MET142 5.0 56.8 1.0

Zinc binding site 4 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1180

b:43.6
occ:1.00
 SG D:CYS140 2.3 49.7 1.0
SG D:CYS176 2.3 62.3 1.0
SG D:CYS143 2.3 62.7 1.0
SG D:CYS173 2.4 64.3 1.0
CB D:CYS140 3.2 47.9 1.0
CB D:CYS143 3.2 67.1 1.0
CB D:CYS176 3.3 60.6 1.0
CB D:CYS173 3.5 54.7 1.0
N D:CYS143 3.7 61.8 1.0
N D:CYS173 4.0 50.1 1.0
CA D:CYS143 4.0 64.9 1.0
CA D:CYS173 4.3 50.8 1.0
OE1 D:GLN146 4.4 73.4 1.0
CA D:CYS176 4.5 60.4 1.0
N D:CYS176 4.5 57.9 1.0
CB D:GLN146 4.6 58.1 1.0
CA D:CYS140 4.6 45.1 1.0
CB D:MET142 4.7 61.1 1.0
C D:CYS143 4.8 64.4 1.0
C D:MET142 4.8 62.6 1.0
N D:HIS144 5.0 64.4 1.0

Zinc binding site 5 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1180

b:40.8
occ:1.00
 SG E:CYS140 2.3 58.8 1.0
SG E:CYS176 2.3 66.6 1.0
SG E:CYS143 2.3 62.5 1.0
SG E:CYS173 2.4 56.5 1.0
CB E:CYS140 3.2 55.8 1.0
CB E:CYS143 3.3 62.5 1.0
CB E:CYS176 3.3 60.6 1.0
CB E:CYS173 3.5 51.0 1.0
N E:CYS143 3.8 60.8 1.0
N E:CYS173 4.0 45.5 1.0
CA E:CYS143 4.1 61.2 1.0
CA E:CYS173 4.3 47.1 1.0
OE1 E:GLN146 4.3 59.0 1.0
CA E:CYS176 4.5 58.1 1.0
N E:CYS176 4.5 55.2 1.0
CB E:GLN146 4.6 54.9 1.0
CA E:CYS140 4.7 54.5 1.0
CB E:MET142 4.8 60.8 1.0
C E:CYS143 4.8 59.5 1.0
C E:MET142 4.9 61.5 1.0
C E:CYS173 5.0 46.3 1.0

Zinc binding site 6 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1182

b:59.7
occ:1.00
 SG F:CYS140 2.3 71.8 1.0
SG F:CYS176 2.3 75.0 1.0
SG F:CYS173 2.3 86.8 1.0
SG F:CYS143 2.4 67.9 1.0
CB F:CYS140 3.2 66.0 1.0
CB F:CYS143 3.3 69.1 1.0
CB F:CYS176 3.3 73.5 1.0
CB F:CYS173 3.4 76.0 1.0
N F:CYS143 3.7 62.1 1.0
N F:CYS173 4.0 68.6 1.0
CA F:CYS143 4.1 63.6 1.0
CA F:CYS173 4.3 71.6 1.0
CA F:CYS176 4.5 72.2 1.0
N F:CYS176 4.5 68.2 1.0
CA F:CYS140 4.7 57.7 1.0
CB F:GLN146 4.7 66.7 1.0
CB F:MET142 4.7 63.1 1.0
C F:CYS143 4.8 60.3 1.0
C F:MET142 4.9 62.8 1.0
C F:CYS173 5.0 70.0 1.0

Zinc binding site 7 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1180

b:31.4
occ:1.00
 SG G:CYS143 2.3 52.1 1.0
SG G:CYS176 2.3 49.3 1.0
SG G:CYS140 2.3 45.7 1.0
SG G:CYS173 2.4 45.9 1.0
CB G:CYS140 3.2 43.8 1.0
CB G:CYS143 3.2 53.9 1.0
CB G:CYS176 3.3 46.5 1.0
CB G:CYS173 3.5 42.1 1.0
N G:CYS143 3.8 49.2 1.0
N G:CYS173 4.0 36.4 1.0
CA G:CYS143 4.1 52.0 1.0
CA G:CYS173 4.3 39.2 1.0
CA G:CYS176 4.5 46.2 1.0
N G:CYS176 4.5 46.4 1.0
CB G:GLN146 4.6 43.9 1.0
CA G:CYS140 4.7 40.2 1.0
CB G:MET142 4.8 45.7 1.0
C G:CYS143 4.8 51.2 1.0
C G:MET142 4.9 48.2 1.0

Zinc binding site 8 out of 8 in 4uxj

Go back to Zinc Binding Sites List in 4uxj
Zinc 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 Zinc with other atoms in the Zn 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:Zn1178

b:64.8
occ:1.00
 SG H:CYS143 2.3 84.5 1.0
SG H:CYS176 2.3 77.5 1.0
SG H:CYS173 2.4 90.7 1.0
SG H:CYS140 2.4 78.6 1.0
CB H:CYS143 3.2 87.5 1.0
CB H:CYS140 3.3 75.8 1.0
CB H:CYS176 3.4 76.2 1.0
CB H:CYS173 3.5 80.4 1.0
N H:CYS143 3.7 79.2 1.0
CA H:CYS143 4.0 83.8 1.0
N H:CYS173 4.1 72.0 1.0
CA H:CYS173 4.4 76.0 1.0
N H:CYS176 4.5 71.9 1.0
CA H:CYS176 4.5 73.8 1.0
CB H:GLN146 4.6 81.6 1.0
CA H:CYS140 4.7 71.2 1.0
CB H:MET142 4.7 74.1 1.0
C H:CYS143 4.8 87.4 1.0
C H:MET142 4.9 78.2 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: Wed Dec 16 05:49:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy