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Magnesium 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:

Bromine (Br) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate, PDB code: 2w0s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2w0s

Go back to Magnesium Binding Sites List in 2w0s
Magnesium binding site 1 out of 4 in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1205

b:41.8
occ:1.00
 OG1 A:THR18 3.0 58.8 1.0
OD2 A:ASP92 3.0 47.8 1.0
ND2 A:ASN37 3.3 48.5 1.0
O2P A:BVP1207 3.3 42.0 1.0
OD1 A:ASN37 3.5 51.6 1.0
CG A:ASN37 3.8 45.7 1.0
CG A:ASP92 3.8 45.5 1.0
O4 A:SO41208 3.9 53.0 1.0
P A:BVP1207 4.2 42.0 1.0
CB A:THR18 4.2 41.3 1.0
OD1 A:ASP92 4.3 42.0 1.0
O1P A:BVP1207 4.3 48.3 1.0
CG2 A:THR18 4.4 39.7 1.0
O3P A:BVP1207 4.4 23.5 1.0
NZ A:LYS17 4.6 54.1 1.0
CB A:ASP92 4.9 37.3 1.0
OH A:TYR35 5.0 54.0 1.0

Magnesium binding site 2 out of 4 in 2w0s

Go back to Magnesium Binding Sites List in 2w0s
Magnesium binding site 2 out of 4 in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg1206

b:27.6
occ:1.00
 OD1 A:ASP13 2.4 31.5 1.0
OE2 A:GLU145 2.5 49.1 1.0
O1P A:BVP1207 3.0 48.3 1.0
O3P A:BVP1207 3.4 23.5 1.0
OE1 A:GLU142 3.4 54.2 1.0
CG A:ASP13 3.7 42.4 1.0
CD A:GLU145 3.7 53.9 1.0
P A:BVP1207 3.7 42.0 1.0
C5' A:BVP1207 4.2 37.0 1.0
CG A:GLU145 4.3 37.4 1.0
O5' A:BVP1207 4.4 40.8 1.0
CD A:GLU142 4.4 59.7 1.0
OD2 A:ASP13 4.4 41.8 1.0
NZ A:LYS14 4.6 56.6 1.0
CE A:LYS14 4.7 51.0 1.0
CB A:ASP13 4.7 51.3 1.0
O2 A:SO41208 4.7 53.9 1.0
OE1 A:GLU145 4.7 64.3 1.0
CB A:GLU142 4.9 50.8 1.0
CG A:GLU142 5.0 52.3 1.0

Magnesium binding site 3 out of 4 in 2w0s

Go back to Magnesium Binding Sites List in 2w0s
Magnesium binding site 3 out of 4 in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1205

b:38.8
occ:1.00
 OD2 B:ASP92 2.7 44.1 1.0
OD1 B:ASN37 3.0 48.5 1.0
ND2 B:ASN37 3.1 49.5 1.0
O1P B:BVP1207 3.3 25.6 1.0
CG B:ASP92 3.3 43.1 1.0
OG1 B:THR18 3.3 55.2 1.0
CG B:ASN37 3.4 47.4 1.0
OD1 B:ASP92 3.8 40.1 1.0
O4 B:SO41208 3.9 53.3 1.0
O2P B:BVP1207 4.0 18.9 1.0
P B:BVP1207 4.1 40.1 1.0
CB B:ASP92 4.2 38.1 1.0
NZ B:LYS17 4.4 55.4 1.0
O3P B:BVP1207 4.4 51.5 1.0
CB B:THR18 4.6 42.9 1.0
O B:PHE38 4.6 32.6 1.0
CG2 B:THR18 4.7 39.7 1.0
OH B:TYR35 4.8 56.9 1.0
CB B:ASN37 5.0 41.6 1.0

Magnesium binding site 4 out of 4 in 2w0s

Go back to Magnesium Binding Sites List in 2w0s
Magnesium binding site 4 out of 4 in the Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Brivudin-5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 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:Mg1206

b:21.1
occ:1.00
 OD1 B:ASP13 2.4 35.0 1.0
O3P B:BVP1207 2.6 51.5 1.0
OE2 B:GLU145 2.9 52.4 1.0
OE1 B:GLU142 3.4 61.1 1.0
P B:BVP1207 3.6 40.1 1.0
CG B:ASP13 3.6 42.4 1.0
C5' B:BVP1207 3.7 31.7 1.0
O2P B:BVP1207 3.9 18.9 1.0
O5' B:BVP1207 4.1 49.0 1.0
CD B:GLU145 4.1 58.7 1.0
OD2 B:ASP13 4.3 42.5 1.0
CD B:GLU142 4.4 61.6 1.0
CG B:GLU145 4.6 44.0 1.0
NH2 B:ARG41 4.7 35.5 1.0
CB B:ASP13 4.7 55.1 1.0
C4' B:BVP1207 4.9 32.1 1.0
O3 B:SO41208 4.9 51.0 1.0
CB B:GLU142 5.0 56.5 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 Aug 14 05:57:22 2024

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