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Bromine in PDB 2w0s: Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate

Enzymatic activity of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate

All present enzymatic activity of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate:
2.7.4.9;

Protein crystallography data

The structure of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate, PDB code: 2w0s was solved by C.Caillat, D.Topalis, L.A.Agrofoglio, S.Pochet, J.Balzarini, D.Deville-Bonne, P.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.852 / 2.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.370, 78.350, 95.040, 90.00, 90.00, 90.00
R / Rfree (%) 21.24 / 28.28

Other elements in 2w0s:

The structure of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate (pdb code 2w0s). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate, PDB code: 2w0s:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in 2w0s

Go back to Bromine Binding Sites List in 2w0s
Bromine binding site 1 out of 3 in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1207

b:43.0
occ:0.63
 BR A:BVP1207 0.0 43.0 0.6
C5B A:BVP1207 1.8 42.2 1.0
OD1 A:ASN65 2.7 61.3 1.0
C5A A:BVP1207 2.9 41.1 1.0
NZ A:LYS105 3.2 52.2 1.0
CG2 A:VAL64 3.4 54.2 1.0
OH A:TYR144 3.5 53.4 1.0
CG A:ASN65 3.7 57.5 1.0
CA A:ALA102 3.8 38.0 1.0
CA A:ASN65 3.9 44.6 1.0
CB A:ALA102 4.0 26.3 1.0
N A:ALA102 4.1 31.7 1.0
N A:ASN65 4.1 47.2 1.0
CE A:LYS105 4.1 56.6 1.0
C5 A:BVP1207 4.1 35.3 1.0
CD2 A:PHE68 4.3 27.5 1.0
CB A:ASN65 4.4 42.7 1.0
C A:VAL64 4.4 41.5 1.0
C A:TYR101 4.5 36.5 1.0
CE2 A:PHE68 4.5 29.0 1.0
ND2 A:ASN65 4.5 60.1 1.0
CZ A:TYR144 4.6 48.9 1.0
O A:TYR101 4.6 41.7 1.0
O A:VAL64 4.6 42.0 1.0
C6 A:BVP1207 4.6 28.3 1.0
CB A:VAL64 4.7 42.5 1.0
CD A:LYS105 4.9 58.8 1.0
CB A:TYR101 4.9 25.0 1.0
O A:GLY98 4.9 40.6 1.0

Bromine binding site 2 out of 3 in 2w0s

Go back to Bromine Binding Sites List in 2w0s
Bromine binding site 2 out of 3 in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1207

b:32.5
occ:0.43
 BR B:BVP1207 0.0 32.5 0.4
C5B B:BVP1207 1.8 37.5 1.0
OD1 B:ASN65 2.8 63.8 1.0
C5A B:BVP1207 2.8 34.0 1.0
NZ B:LYS105 3.1 53.7 1.0
CA B:ALA102 3.5 38.3 1.0
N B:ALA102 3.6 28.4 1.0
OH B:TYR144 3.6 52.4 1.0
CG B:ASN65 3.8 60.3 1.0
CB B:ALA102 3.8 30.8 1.0
CG2 B:VAL64 3.8 47.0 1.0
C B:TYR101 4.0 36.5 1.0
CE B:LYS105 4.1 56.8 1.0
C5 B:BVP1207 4.1 33.0 1.0
O B:TYR101 4.2 37.3 1.0
CA B:ASN65 4.2 43.0 1.0
N B:ASN65 4.4 49.7 1.0
CB B:TYR101 4.5 26.9 1.0
CZ B:TYR144 4.5 51.1 1.0
CD2 B:PHE68 4.5 33.6 1.0
ND2 B:ASN65 4.6 62.9 1.0
CB B:ASN65 4.6 46.9 1.0
C6 B:BVP1207 4.6 29.6 1.0
CD B:LYS105 4.6 53.5 1.0
O B:GLY98 4.7 40.4 1.0
CE2 B:PHE68 4.8 29.6 1.0
C B:ALA102 4.9 46.7 1.0
C B:VAL64 4.9 44.3 1.0
CA B:TYR101 4.9 33.6 1.0

Bromine binding site 3 out of 3 in 2w0s

Go back to Bromine Binding Sites List in 2w0s
Bromine binding site 3 out of 3 in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1209

b:91.2
occ:1.00
 BR B:BVP1209 0.0 91.2 1.0
C5B B:BVP1209 1.9 56.4 1.0
C5A B:BVP1209 2.8 52.5 1.0
O B:LEU66 3.8 38.0 1.0
CB B:ALA70 3.9 28.1 1.0
N B:ALA70 3.9 24.8 1.0
CA B:ALA70 4.1 32.9 1.0
C5 B:BVP1209 4.2 41.4 1.0
CB B:LEU66 4.2 43.4 1.0
CB B:CYS69 4.2 33.6 1.0
CD2 B:LEU66 4.4 42.0 1.0
SG B:CYS69 4.5 46.6 1.0
O4 B:BVP1209 4.6 61.3 1.0
CA B:LEU66 4.6 37.2 1.0
C B:LEU66 4.7 35.2 1.0
C B:CYS69 4.7 36.8 1.0
C4 B:BVP1209 4.8 45.0 1.0
CG B:LEU66 4.9 58.7 1.0

Reference:

C.Caillat, D.Topalis, L.A.Agrofoglio, S.Pochet, J.Balzarini, D.Deville-Bonne, P.Meyer. Crystal Structure of Poxvirus Thymidylate Kinase: An Unexpected Dimerization Has Implications For Antiviral Therapy Proc.Natl.Acad.Sci.Usa V. 105 16900 2008.
ISSN: ISSN 0027-8424
PubMed: 18971333
DOI: 10.1073/PNAS.0804525105
Page generated: Wed Jul 10 18:46:09 2024

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