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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights For Drug Design, PDB code: 2j87:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2j87

Go back to Magnesium Binding Sites List in 2j87
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg500

b:15.6
occ:1.00
 O3B A:TTP300 2.1 47.9 1.0
O1A A:TTP300 2.4 45.1 1.0
PB A:TTP300 2.8 50.2 1.0
O3A A:TTP300 2.8 48.4 1.0
O3G A:TTP300 2.9 47.3 1.0
PG A:TTP300 3.0 47.0 1.0
O2B A:TTP300 3.1 50.3 1.0
PA A:TTP300 3.2 46.4 1.0
N A:PHE14 3.5 43.2 1.0
CB A:MET13 3.7 43.5 1.0
O2G A:TTP300 3.8 46.9 1.0
O5' A:TTP300 3.9 46.6 1.0
CA A:MET13 4.1 43.4 1.0
CD1 A:PHE14 4.2 42.9 1.0
O1G A:TTP300 4.3 45.7 1.0
O1B A:TTP300 4.3 50.4 1.0
C A:MET13 4.3 43.4 1.0
CA A:PHE14 4.4 43.2 1.0
CE A:MET13 4.5 43.0 1.0
O2A A:TTP300 4.5 46.1 1.0
CE1 A:PHE14 4.6 43.1 1.0
CG A:MET13 4.6 43.4 1.0
SD A:MET13 4.7 43.4 1.0
CG A:PHE14 5.0 43.2 1.0

Magnesium binding site 2 out of 4 in 2j87

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg500

b:22.2
occ:1.00
 O1A B:TTP300 1.7 26.6 1.0
O3G B:TTP300 1.9 35.9 1.0
O2B B:TTP300 2.2 37.4 1.0
PA B:TTP300 2.8 28.2 1.0
O2A B:TTP300 3.0 27.4 1.0
PG B:TTP300 3.1 35.7 1.0
PB B:TTP300 3.2 37.3 1.0
N B:PHE14 3.3 43.3 1.0
CB B:MET13 3.5 43.4 1.0
O3B B:TTP300 3.5 36.2 1.0
O3A B:TTP300 3.6 32.4 1.0
O2G B:TTP300 3.7 33.9 1.0
CA B:MET13 3.8 43.3 1.0
C B:MET13 4.1 43.3 1.0
O5' B:TTP300 4.2 29.2 1.0
O1G B:TTP300 4.3 36.0 1.0
CA B:PHE14 4.3 43.3 1.0
CD1 B:PHE14 4.3 42.9 1.0
CG B:MET13 4.4 43.5 1.0
CE B:MET13 4.5 43.0 1.0
O1B B:TTP300 4.6 38.0 1.0
CE1 B:PHE14 4.7 43.1 1.0
C5' B:TTP300 4.7 29.9 1.0
SD B:MET13 4.7 43.5 1.0
NZ B:LYS17 4.8 43.0 1.0
CG B:PHE14 4.9 43.1 1.0

Magnesium binding site 3 out of 4 in 2j87

Go back to Magnesium Binding Sites List in 2j87
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg500

b:6.0
occ:1.00
 O3A C:TTP300 2.0 32.0 1.0
O1A C:TTP300 2.3 30.3 1.0
O3G C:TTP300 2.4 31.3 1.0
PA C:TTP300 2.4 31.0 1.0
O5' C:TTP300 2.5 31.4 1.0
PB C:TTP300 2.9 33.4 1.0
O2B C:TTP300 3.0 34.0 1.0
O3B C:TTP300 3.2 33.1 1.0
PG C:TTP300 3.3 33.8 1.0
CB C:MET13 3.6 43.4 1.0
C5' C:TTP300 3.8 32.9 1.0
O2A C:TTP300 3.9 29.9 1.0
CA C:MET13 4.0 43.3 1.0
N C:PHE14 4.0 43.2 1.0
O2G C:TTP300 4.1 33.1 1.0
CG C:MET13 4.2 43.4 1.0
CE C:MET13 4.3 43.2 1.0
O1B C:TTP300 4.3 32.8 1.0
SD C:MET13 4.3 43.6 1.0
O1G C:TTP300 4.5 35.2 1.0
NZ C:LYS17 4.6 43.0 1.0
C C:MET13 4.6 43.3 1.0
C3' C:TTP300 4.8 36.9 1.0
C4' C:TTP300 4.8 34.8 1.0
CD1 C:PHE14 5.0 42.8 1.0

Magnesium binding site 4 out of 4 in 2j87

Go back to Magnesium Binding Sites List in 2j87
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg500

b:21.6
occ:1.00
 O3B D:TTP300 1.9 39.5 1.0
O3A D:TTP300 2.2 39.5 1.0
O1A D:TTP300 2.6 37.8 1.0
PB D:TTP300 2.6 40.5 1.0
PA D:TTP300 2.8 37.4 1.0
O5' D:TTP300 3.2 38.9 1.0
PG D:TTP300 3.3 40.0 1.0
O2B D:TTP300 3.4 41.9 1.0
CB D:MET13 3.7 43.4 1.0
O1G D:TTP300 3.8 41.1 1.0
O3G D:TTP300 3.8 38.9 1.0
N D:PHE14 3.8 43.2 1.0
O1B D:TTP300 4.0 41.2 1.0
O2A D:TTP300 4.2 38.1 1.0
CA D:MET13 4.2 43.3 1.0
CE D:MET13 4.3 43.1 1.0
O2G D:TTP300 4.4 40.7 1.0
CD1 D:PHE14 4.4 42.8 1.0
CG D:MET13 4.5 43.4 1.0
C D:MET13 4.6 43.3 1.0
SD D:MET13 4.6 43.3 1.0
C5' D:TTP300 4.6 42.3 1.0
CE1 D:PHE14 4.6 43.0 1.0
CA D:PHE14 4.8 43.3 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: Mon Dec 14 07:28:56 2020

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