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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2wvj

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Zinc binding site 1 out of 8 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 Zinc with other atoms in the Zn 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
A:Zn1193

b:19.3
occ:1.00
SG A:CYS153 2.3 16.2 1.0
SG A:CYS185 2.3 15.4 1.0
SG A:CYS156 2.3 21.8 1.0
SG A:CYS188 2.4 19.5 1.0
CB A:CYS156 3.2 22.6 1.0
CB A:CYS188 3.2 19.7 1.0
CB A:CYS153 3.3 16.6 1.0
CB A:CYS185 3.5 16.4 1.0
N A:CYS156 3.7 22.3 1.0
N A:CYS185 3.9 15.9 1.0
CA A:CYS156 4.0 22.7 1.0
N A:CYS188 4.3 19.4 1.0
CA A:CYS185 4.3 16.2 1.0
CA A:CYS188 4.3 19.8 1.0
C A:CYS156 4.6 23.0 1.0
O A:HOH2115 4.6 35.4 1.0
NH2 C:ARG18 4.6 32.6 1.0
N A:PHE157 4.7 23.3 1.0
C A:GLU155 4.7 22.0 1.0
CA A:CYS153 4.8 16.9 1.0
C A:CYS185 4.9 16.5 1.0
CB A:GLU155 5.0 21.8 1.0
N A:ARG158 5.0 23.5 1.0
C A:VAL184 5.0 15.7 1.0
O A:CYS185 5.0 16.5 1.0

Zinc binding site 2 out of 8 in 2wvj

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Zinc binding site 2 out of 8 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 Zinc with other atoms in the Zn 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
B:Zn1194

b:17.4
occ:1.00
SG B:CYS153 2.2 15.8 1.0
SG B:CYS156 2.3 20.9 1.0
SG B:CYS185 2.4 16.0 1.0
SG B:CYS188 2.4 19.8 1.0
CB B:CYS156 3.2 21.6 1.0
CB B:CYS188 3.3 19.5 1.0
CB B:CYS153 3.3 16.6 1.0
CB B:CYS185 3.5 16.1 1.0
N B:CYS156 3.6 21.4 1.0
N B:CYS185 3.8 15.9 1.0
CA B:CYS156 3.9 21.9 1.0
CA B:CYS185 4.2 16.2 1.0
N B:CYS188 4.3 19.4 1.0
CA B:CYS188 4.4 19.8 1.0
NH2 D:ARG18 4.4 36.6 1.0
C B:CYS156 4.5 22.3 1.0
O B:HOH2034 4.5 60.1 1.0
C B:GLU155 4.6 21.1 1.0
N B:PHE157 4.6 23.0 1.0
CA B:CYS153 4.7 16.8 1.0
C B:CYS185 4.9 16.1 1.0
CB B:GLU155 4.9 20.8 1.0
N B:ARG158 4.9 24.0 1.0
C B:VAL184 5.0 16.2 1.0

Zinc binding site 3 out of 8 in 2wvj

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Zinc binding site 3 out of 8 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 Zinc with other atoms in the Zn 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
C:Zn1193

b:25.3
occ:1.00
SG C:CYS153 2.2 19.0 1.0
SG C:CYS156 2.4 26.6 1.0
SG C:CYS188 2.4 24.3 1.0
SG C:CYS185 2.5 19.2 1.0
CB C:CYS156 3.2 26.0 1.0
CB C:CYS153 3.3 19.9 1.0
CB C:CYS188 3.3 23.6 1.0
CB C:CYS185 3.4 18.6 1.0
N C:CYS156 3.7 25.9 1.0
N C:CYS185 3.8 18.5 1.0
CA C:CYS156 4.0 26.2 1.0
CA C:CYS185 4.2 18.7 1.0
N C:CYS188 4.4 23.2 1.0
CA C:CYS188 4.4 23.7 1.0
C C:CYS156 4.5 26.5 1.0
NH2 A:ARG18 4.6 34.5 1.0
N C:PHE157 4.6 26.8 1.0
C C:GLU155 4.7 25.3 1.0
CA C:CYS153 4.7 20.0 1.0
C C:CYS185 4.8 18.7 1.0
N C:ARG158 4.9 26.7 1.0
O C:CYS185 5.0 18.5 1.0
CB C:GLU155 5.0 24.7 1.0
C C:VAL184 5.0 18.6 1.0

Zinc binding site 4 out of 8 in 2wvj

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Zinc binding site 4 out of 8 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 Zinc with other atoms in the Zn binding site number 4 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:Zn1194

b:21.2
occ:1.00
SG D:CYS153 2.2 16.0 1.0
SG D:CYS188 2.3 21.0 1.0
SG D:CYS156 2.4 23.1 1.0
SG D:CYS185 2.4 18.4 1.0
CB D:CYS188 3.2 20.9 1.0
CB D:CYS156 3.2 23.2 1.0
CB D:CYS153 3.3 17.1 1.0
CB D:CYS185 3.5 18.1 1.0
N D:CYS156 3.7 23.1 1.0
N D:CYS185 3.9 17.6 1.0
CA D:CYS156 4.0 23.4 1.0
N D:CYS188 4.3 20.8 1.0
CA D:CYS185 4.3 18.1 1.0
CA D:CYS188 4.3 20.9 1.0
NH2 B:ARG18 4.4 37.0 1.0
O B:HOH2004 4.4 38.8 1.0
C D:GLU155 4.5 22.8 1.0
C D:CYS156 4.6 23.7 1.0
CA D:CYS153 4.7 17.2 1.0
N D:PHE157 4.7 24.1 1.0
CB D:GLU155 4.8 22.6 1.0
C D:CYS185 4.9 18.4 1.0
O D:CYS185 5.0 18.7 1.0
CA D:GLU155 5.0 22.6 1.0

Zinc binding site 5 out of 8 in 2wvj

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Zinc binding site 5 out of 8 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 Zinc with other atoms in the Zn binding site number 5 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
E:Zn1193

b:21.0
occ:1.00
SG E:CYS156 2.2 23.2 1.0
SG E:CYS153 2.2 17.6 1.0
SG E:CYS185 2.4 19.1 1.0
SG E:CYS188 2.4 21.3 1.0
CB E:CYS188 3.2 21.2 1.0
CB E:CYS156 3.2 23.3 1.0
CB E:CYS153 3.3 17.6 1.0
CB E:CYS185 3.5 18.4 1.0
N E:CYS156 3.7 23.1 1.0
N E:CYS185 3.9 17.9 1.0
CA E:CYS156 4.0 23.4 1.0
N E:CYS188 4.2 21.2 1.0
NH2 G:ARG18 4.3 37.2 1.0
CA E:CYS185 4.3 18.3 1.0
CA E:CYS188 4.3 21.3 1.0
C E:CYS156 4.6 23.7 1.0
C E:GLU155 4.6 22.8 1.0
N E:PHE157 4.7 24.2 1.0
CA E:CYS153 4.8 17.9 1.0
CB E:GLU155 4.9 22.3 1.0
C E:CYS185 4.9 18.4 1.0

Zinc binding site 6 out of 8 in 2wvj

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Zinc binding site 6 out of 8 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 Zinc with other atoms in the Zn binding site number 6 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
F:Zn1193

b:21.0
occ:1.00
SG F:CYS153 2.3 16.8 1.0
SG F:CYS185 2.3 15.6 1.0
SG F:CYS156 2.4 22.8 1.0
SG F:CYS188 2.4 18.0 1.0
CB F:CYS156 3.2 23.2 1.0
CB F:CYS188 3.2 18.4 1.0
CB F:CYS153 3.3 17.8 1.0
CB F:CYS185 3.5 16.0 1.0
N F:CYS156 3.6 22.7 1.0
N F:CYS185 3.9 16.0 1.0
CA F:CYS156 3.9 23.2 1.0
N F:CYS188 4.3 18.4 1.0
CA F:CYS185 4.3 16.1 1.0
NH2 H:ARG18 4.3 38.0 1.0
CA F:CYS188 4.4 18.4 1.0
O H:HOH2004 4.4 42.8 1.0
C F:GLU155 4.5 22.2 1.0
C F:CYS156 4.6 23.6 1.0
N F:PHE157 4.6 24.3 1.0
CA F:CYS153 4.8 17.7 1.0
CB F:GLU155 4.8 21.9 1.0
C F:CYS185 4.9 15.8 1.0
CA F:GLU155 5.0 21.9 1.0
C F:VAL184 5.0 16.5 1.0

Zinc binding site 7 out of 8 in 2wvj

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Zinc binding site 7 out of 8 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 Zinc with other atoms in the Zn binding site number 7 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:Zn1194

b:18.3
occ:1.00
SG G:CYS156 2.2 20.3 1.0
SG G:CYS153 2.3 14.8 1.0
SG G:CYS185 2.3 15.4 1.0
SG G:CYS188 2.4 19.2 1.0
CB G:CYS156 3.1 21.9 1.0
CB G:CYS188 3.2 19.8 1.0
CB G:CYS153 3.4 15.9 1.0
CB G:CYS185 3.5 16.1 1.0
N G:CYS156 3.7 21.6 1.0
N G:CYS185 3.9 15.8 1.0
CA G:CYS156 3.9 21.8 1.0
N G:CYS188 4.2 19.7 1.0
CA G:CYS185 4.3 16.2 1.0
CA G:CYS188 4.3 19.9 1.0
C G:CYS156 4.5 22.3 1.0
C G:GLU155 4.6 21.4 1.0
NH2 E:ARG18 4.6 35.7 1.0
N G:PHE157 4.7 22.8 1.0
CA G:CYS153 4.8 16.1 1.0
C G:CYS185 4.9 16.6 1.0
CB G:GLU155 4.9 21.2 1.0
O G:CYS185 4.9 16.5 1.0
C G:VAL184 5.0 15.7 1.0

Zinc binding site 8 out of 8 in 2wvj

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Zinc binding site 8 out of 8 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 Zinc with other atoms in the Zn binding site number 8 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:Zn1194

b:20.4
occ:1.00
SG H:CYS156 2.3 23.1 1.0
SG H:CYS153 2.3 16.5 1.0
SG H:CYS188 2.4 19.5 1.0
SG H:CYS185 2.4 17.1 1.0
CB H:CYS156 3.2 22.3 1.0
CB H:CYS188 3.2 19.3 1.0
CB H:CYS153 3.3 17.1 1.0
CB H:CYS185 3.6 16.5 1.0
N H:CYS156 3.7 22.2 1.0
N H:CYS185 3.9 16.3 1.0
CA H:CYS156 3.9 22.4 1.0
N H:CYS188 4.2 19.7 1.0
CA H:CYS185 4.3 16.6 1.0
NH2 F:ARG18 4.3 32.9 1.0
CA H:CYS188 4.3 19.4 1.0
C H:CYS156 4.6 22.5 1.0
C H:GLU155 4.6 22.1 1.0
N H:PHE157 4.7 22.9 1.0
CA H:CYS153 4.8 17.1 1.0
CB H:GLU155 4.8 22.0 1.0
C H:CYS185 5.0 16.7 1.0
C H:VAL184 5.0 16.3 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: Sat Sep 26 04:26:49 2020
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