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Magnesium in PDB 2wvj: Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine

Enzymatic activity of Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine

All present enzymatic activity of Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine:
2.7.1.21;

Protein crystallography data

The structure of Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine, PDB code: 2wvj was solved by T.Skovgaard, U.Uhlin, B.Munch-Petersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.81 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.902, 123.252, 121.024, 90.00, 132.98, 90.00
R / Rfree (%) 17.3 / 22.1

Other elements in 2wvj:

The structure of Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine (pdb code 2wvj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine, PDB code: 2wvj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2wvj

Go back to Magnesium Binding Sites List in 2wvj
Magnesium binding site 1 out of 3 in the Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1193

b:46.0
occ:1.00
O1A D:TTP1192 1.9 19.2 1.0
O D:HOH2057 2.6 29.8 1.0
O2G D:TTP1192 2.6 20.1 1.0
OG D:SER33 2.6 15.7 1.0
O1B D:TTP1192 2.9 23.7 1.0
O D:HOH2009 2.9 21.6 1.0
O D:HOH2056 3.1 15.9 1.0
O3B D:TTP1192 3.1 23.5 1.0
PA D:TTP1192 3.2 20.3 1.0
PG D:TTP1192 3.4 20.7 1.0
PB D:TTP1192 3.4 23.3 1.0
O3A D:TTP1192 3.6 22.0 1.0
CB D:SER33 3.7 13.4 1.0
O D:HOH2137 4.2 31.6 1.0
O2A D:TTP1192 4.2 18.4 1.0
OD1 D:ASP97 4.2 17.7 1.0
O5' D:TTP1192 4.3 19.0 1.0
OD2 D:ASP97 4.4 18.5 1.0
O1G D:TTP1192 4.4 22.6 1.0
O3G D:TTP1192 4.4 20.9 1.0
OE2 D:GLU98 4.5 17.9 1.0
N D:SER33 4.6 12.5 1.0
NH2 D:ARG60 4.6 26.1 1.0
O D:HOH2136 4.6 17.0 1.0
O D:HOH2074 4.6 33.3 1.0
CG D:ASP97 4.7 16.9 1.0
CA D:SER33 4.8 13.3 1.0
CG D:GLU98 4.8 16.3 1.0
O2B D:TTP1192 4.9 23.1 1.0

Magnesium binding site 2 out of 3 in 2wvj

Go back to Magnesium Binding Sites List in 2wvj
Magnesium binding site 2 out of 3 in the Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1193

b:23.5
occ:1.00
O1A G:TTP1192 2.2 15.8 1.0
O G:HOH2092 2.4 20.4 1.0
O1B G:TTP1192 2.5 19.2 1.0
O G:HOH2014 2.5 30.0 1.0
O3G G:TTP1192 2.6 15.6 1.0
OG G:SER33 2.6 13.4 1.0
PB G:TTP1192 3.4 18.4 1.0
O3B G:TTP1192 3.5 19.3 1.0
PA G:TTP1192 3.5 18.0 1.0
PG G:TTP1192 3.6 17.1 1.0
CB G:SER33 3.6 11.4 1.0
O3A G:TTP1192 3.9 17.8 1.0
O G:HOH2093 4.0 16.9 1.0
NH2 G:ARG60 4.4 25.5 1.0
OD1 G:ASP97 4.4 17.4 1.0
OD2 G:ASP97 4.4 18.5 1.0
O G:HOH2162 4.4 15.0 1.0
O2G G:TTP1192 4.5 16.4 1.0
O5' G:TTP1192 4.5 16.8 1.0
O2A G:TTP1192 4.5 16.1 1.0
N G:SER33 4.6 10.8 1.0
OE2 G:GLU98 4.6 19.5 1.0
O1G G:TTP1192 4.7 15.8 1.0
CA G:SER33 4.7 11.2 1.0
O2B G:TTP1192 4.8 19.9 1.0
CG G:ASP97 4.9 17.0 1.0
O G:HOH2065 5.0 31.8 1.0

Magnesium binding site 3 out of 3 in 2wvj

Go back to Magnesium Binding Sites List in 2wvj
Magnesium binding site 3 out of 3 in the Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mutation of THR163 to Ser in Human Thymidine Kinase Shifts the Specificity From Thymidine Towards the Nucleoside Analogue Azidothymidine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1193

b:27.1
occ:1.00
O1A H:TTP1192 2.0 15.8 1.0
OG H:SER33 2.5 13.6 1.0
O H:HOH2077 2.6 19.0 1.0
O2G H:TTP1192 2.7 16.7 1.0
O H:HOH2013 2.7 24.8 1.0
O1B H:TTP1192 2.7 22.1 1.0
O3B H:TTP1192 3.0 21.3 1.0
PB H:TTP1192 3.3 21.4 1.0
PA H:TTP1192 3.4 18.6 1.0
PG H:TTP1192 3.4 17.1 1.0
O H:HOH2153 3.7 28.8 1.0
CB H:SER33 3.7 10.7 1.0
O3A H:TTP1192 3.7 20.0 1.0
O H:HOH2075 4.0 18.5 1.0
OD1 H:ASP97 4.3 15.2 1.0
O5' H:TTP1192 4.3 17.9 1.0
O2A H:TTP1192 4.4 15.0 1.0
O1G H:TTP1192 4.4 19.6 1.0
OD2 H:ASP97 4.4 17.6 1.0
OE2 H:GLU98 4.5 18.9 1.0
O3G H:TTP1192 4.5 17.8 1.0
N H:SER33 4.5 10.2 1.0
NH2 H:ARG60 4.6 26.2 1.0
O H:HOH2150 4.6 12.5 1.0
CA H:SER33 4.7 10.9 1.0
O2B H:TTP1192 4.7 22.1 1.0
CG H:ASP97 4.8 15.1 1.0
O H:HOH2076 4.8 38.8 1.0

Reference:

T.Skovgaard, U.Uhlin, B.Munch-Petersen. Comparative Active-Site Mutation Study of Human and Caenorhabditis Elegans Thymidine Kinase 1. Febs J. V. 279 1777 2012.
ISSN: ISSN 1742-464X
PubMed: 22385435
DOI: 10.1111/J.1742-4658.2012.08554.X
Page generated: Wed Aug 14 06:17:38 2024

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