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Zinc in PDB 2j87: Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design

Enzymatic activity of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design

All present enzymatic activity of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design:
2.7.1.21;

Protein crystallography data

The structure of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design, PDB code: 2j87 was solved by K.El Omari, N.Solaroli, A.Karlsson, J.Balzarini, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.10
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 63.331, 63.331, 166.412, 90.00, 90.00, 120.00
R / Rfree (%) 25.7 / 28.9

Other elements in 2j87:

The structure of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design (pdb code 2j87). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design, PDB code: 2j87:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2j87

Go back to Zinc Binding Sites List in 2j87
Zinc binding site 1 out of 4 in the Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:52.3
occ:1.00
 SG A:CYS173 2.2 41.0 1.0
SG A:CYS138 2.3 42.3 1.0
SG A:CYS170 2.3 42.7 1.0
SG A:CYS141 2.7 42.2 1.0
CB A:CYS170 3.0 42.8 1.0
CB A:CYS138 3.3 42.5 1.0
CB A:CYS141 3.3 42.6 1.0
CB A:CYS173 3.3 42.5 1.0
N A:CYS170 3.4 43.0 1.0
N A:CYS141 3.5 42.9 1.0
CA A:CYS170 3.7 42.9 1.0
CA A:CYS141 3.9 42.7 1.0
CB A:LYS140 4.3 43.3 1.0
N A:CYS173 4.4 42.9 1.0
C A:CYS170 4.4 42.9 1.0
CA A:CYS173 4.5 42.6 1.0
C A:CYS141 4.5 42.8 1.0
C A:VAL169 4.5 43.0 1.0
N A:PHE142 4.6 42.7 1.0
O A:CYS170 4.6 42.8 1.0
C A:LYS140 4.6 43.0 1.0
CA A:CYS138 4.7 42.5 1.0
CA A:VAL169 4.8 43.0 1.0
CA A:LYS140 4.8 43.1 1.0
N A:LYS140 4.9 43.0 1.0
N A:LYS143 5.0 42.7 1.0
CB A:VAL169 5.0 43.0 1.0

Zinc binding site 2 out of 4 in 2j87

Go back to Zinc Binding Sites List in 2j87
Zinc binding site 2 out of 4 in the Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:49.7
occ:1.00
 SG B:CYS138 2.0 42.3 1.0
SG B:CYS173 2.3 41.1 1.0
SG B:CYS141 2.4 42.3 1.0
SG B:CYS170 2.6 42.6 1.0
N B:CYS141 3.0 42.9 1.0
CB B:CYS138 3.0 42.4 1.0
CB B:CYS141 3.1 42.7 1.0
CB B:CYS170 3.4 42.8 1.0
CB B:CYS173 3.5 42.5 1.0
CA B:CYS141 3.5 42.8 1.0
N B:CYS170 3.6 43.0 1.0
CB B:LYS140 4.0 43.3 1.0
CA B:CYS170 4.1 42.9 1.0
C B:LYS140 4.1 43.0 1.0
N B:PHE142 4.1 42.7 1.0
C B:CYS141 4.2 42.8 1.0
CA B:LYS140 4.4 43.1 1.0
CA B:CYS138 4.4 42.4 1.0
N B:LYS140 4.4 43.0 1.0
N B:LYS143 4.7 42.8 1.0
C B:VAL169 4.7 43.0 1.0
CA B:CYS173 4.7 42.6 1.0
C B:CYS138 4.8 42.7 1.0
N B:CYS173 4.8 43.0 1.0
C B:CYS170 4.8 43.0 1.0
CA B:VAL169 4.8 43.0 1.0
O B:CYS170 4.9 42.9 1.0

Zinc binding site 3 out of 4 in 2j87

Go back to Zinc Binding Sites List in 2j87
Zinc binding site 3 out of 4 in the Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:48.1
occ:1.00
 SG C:CYS141 2.2 42.3 1.0
SG C:CYS173 2.3 41.0 1.0
SG C:CYS138 2.3 42.2 1.0
SG C:CYS170 2.4 42.4 1.0
CB C:CYS141 3.0 42.6 1.0
CB C:CYS170 3.2 42.8 1.0
N C:CYS141 3.2 42.8 1.0
CB C:CYS138 3.2 42.5 1.0
CA C:CYS141 3.6 42.8 1.0
CB C:CYS173 3.6 42.6 1.0
N C:CYS170 3.7 43.0 1.0
CA C:CYS170 4.0 42.9 1.0
C C:CYS141 4.1 42.8 1.0
N C:PHE142 4.2 42.7 1.0
CB C:LYS140 4.3 43.3 1.0
C C:LYS140 4.4 43.0 1.0
CA C:CYS138 4.6 42.5 1.0
N C:LYS143 4.7 42.7 1.0
CA C:LYS140 4.7 43.1 1.0
N C:CYS173 4.7 42.9 1.0
C C:CYS170 4.8 43.0 1.0
N C:LYS140 4.8 43.0 1.0
CA C:CYS173 4.8 42.6 1.0
C C:VAL169 4.8 43.0 1.0
O C:CYS141 5.0 43.0 1.0
O C:CYS170 5.0 42.9 1.0

Zinc binding site 4 out of 4 in 2j87

Go back to Zinc Binding Sites List in 2j87
Zinc binding site 4 out of 4 in the Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn400

b:45.8
occ:1.00
 SG D:CYS141 2.2 42.5 1.0
SG D:CYS138 2.3 42.1 1.0
SG D:CYS170 2.4 42.3 1.0
SG D:CYS173 2.4 40.9 1.0
CB D:CYS141 3.1 42.6 1.0
CB D:CYS138 3.1 42.4 1.0
CB D:CYS170 3.1 42.8 1.0
N D:CYS141 3.3 42.9 1.0
CB D:CYS173 3.6 42.4 1.0
N D:CYS170 3.6 43.0 1.0
CA D:CYS141 3.6 42.7 1.0
CA D:CYS170 4.0 42.8 1.0
C D:CYS141 4.2 42.7 1.0
N D:PHE142 4.2 42.6 1.0
CB D:LYS140 4.3 43.2 1.0
C D:LYS140 4.4 43.1 1.0
CA D:CYS138 4.6 42.4 1.0
N D:LYS143 4.6 42.8 1.0
N D:CYS173 4.7 42.9 1.0
C D:CYS170 4.7 42.9 1.0
CA D:LYS140 4.7 43.1 1.0
C D:VAL169 4.8 43.0 1.0
CA D:CYS173 4.8 42.5 1.0
N D:LYS140 4.8 42.9 1.0
O D:CYS170 4.9 42.9 1.0
O D:LYS143 5.0 43.0 1.0
CA D:VAL169 5.0 43.0 1.0
O D:CYS141 5.0 42.9 1.0

Reference:

K.El Omari, N.Solaroli, A.Karlsson, J.Balzarini, D.K.Stammers. Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design. Bmc Struct.Biol. V. 6 22 2006.
ISSN: ISSN 1472-6807
PubMed: 17062140
DOI: 10.1186/1472-6807-6-22
Page generated: Thu Oct 17 01:07:40 2024

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