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Zinc in PDB 1xbt: Crystal Structure of Human Thymidine Kinase 1

Enzymatic activity of Crystal Structure of Human Thymidine Kinase 1

All present enzymatic activity of Crystal Structure of Human Thymidine Kinase 1:
2.7.1.21;

Protein crystallography data

The structure of Crystal Structure of Human Thymidine Kinase 1, PDB code: 1xbt was solved by M.Welin, U.Kosinska, N.E.Mikkelsen, C.Carnrot, C.Zhu, L.Wang, S.Eriksson, B.Munch-Petersen, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.07 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.672, 123.177, 116.000, 90.00, 130.20, 90.00
R / Rfree (%) 20.1 / 23.2

Other elements in 1xbt:

The structure of Crystal Structure of Human Thymidine Kinase 1 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Thymidine Kinase 1 (pdb code 1xbt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human Thymidine Kinase 1, PDB code: 1xbt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1xbt

Go back to Zinc Binding Sites List in 1xbt
Zinc binding site 1 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1193

b:31.5
occ:1.00
 SG A:CYS153 2.3 30.3 1.0
SG A:CYS185 2.3 29.4 1.0
SG A:CYS156 2.4 38.2 1.0
SG A:CYS188 2.4 36.3 1.0
CB A:CYS156 3.2 38.0 1.0
CB A:CYS188 3.2 34.6 1.0
CB A:CYS153 3.4 31.7 1.0
CB A:CYS185 3.5 30.0 1.0
N A:CYS156 3.8 37.9 1.0
N A:CYS185 3.9 29.6 1.0
CA A:CYS156 4.0 38.0 1.0
N A:CYS188 4.2 34.6 1.0
CA A:CYS185 4.2 30.0 1.0
NH2 C:ARG18 4.3 55.4 1.0
CA A:CYS188 4.3 34.8 1.0
C A:CYS156 4.6 38.1 1.0
O A:HOH1215 4.7 43.1 1.0
C A:GLU155 4.8 37.8 1.0
N A:PHE157 4.8 38.4 1.0
CA A:CYS153 4.8 31.9 1.0
C A:CYS185 4.8 30.4 1.0
CB A:GLU155 5.0 37.7 1.0
O A:CYS185 5.0 30.2 1.0

Zinc binding site 2 out of 8 in 1xbt

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Zinc binding site 2 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2193

b:30.5
occ:1.00
 SG B:CYS156 2.2 36.7 1.0
SG B:CYS188 2.2 34.4 1.0
SG B:CYS153 2.3 30.3 1.0
SG B:CYS185 2.4 29.0 1.0
CB B:CYS156 3.1 37.5 1.0
CB B:CYS153 3.3 31.2 1.0
CB B:CYS188 3.3 34.3 1.0
CB B:CYS185 3.5 29.7 1.0
N B:CYS156 3.7 37.8 1.0
CA B:CYS156 3.9 37.8 1.0
N B:CYS185 3.9 29.6 1.0
CA B:CYS185 4.3 30.0 1.0
N B:CYS188 4.3 34.5 1.0
CA B:CYS188 4.4 34.7 1.0
C B:CYS156 4.5 38.1 1.0
NH2 D:ARG18 4.5 55.8 1.0
C B:GLU155 4.6 37.7 1.0
N B:PHE157 4.6 38.5 1.0
CA B:CYS153 4.8 31.8 1.0
N B:ARG158 4.9 38.8 1.0
C B:CYS185 5.0 30.2 1.0
CB B:GLU155 5.0 37.4 1.0

Zinc binding site 3 out of 8 in 1xbt

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Zinc binding site 3 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3193

b:41.3
occ:1.00
 SG C:CYS156 2.0 39.7 1.0
SG C:CYS153 2.3 33.2 1.0
SG C:CYS185 2.4 32.5 1.0
SG C:CYS188 2.5 38.6 1.0
CB C:CYS156 3.1 38.1 1.0
CB C:CYS153 3.1 32.2 1.0
CB C:CYS188 3.3 35.2 1.0
CB C:CYS185 3.5 30.2 1.0
N C:CYS156 3.6 37.9 1.0
CA C:CYS156 3.9 38.0 1.0
N C:CYS185 3.9 29.6 1.0
CA C:CYS185 4.3 30.1 1.0
N C:CYS188 4.4 34.7 1.0
CA C:CYS188 4.4 35.1 1.0
C C:CYS156 4.5 38.2 1.0
C C:GLU155 4.6 37.7 1.0
N C:PHE157 4.6 38.5 1.0
CA C:CYS153 4.6 32.1 1.0
NH2 A:ARG18 4.7 56.6 1.0
CB C:GLU155 4.9 37.7 1.0
N C:ARG158 4.9 38.9 1.0
C C:CYS185 5.0 30.4 1.0
C C:VAL184 5.0 29.5 1.0
N C:GLU155 5.0 36.9 1.0

Zinc binding site 4 out of 8 in 1xbt

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Zinc binding site 4 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4193

b:36.1
occ:1.00
 SG D:CYS153 2.3 31.7 1.0
SG D:CYS185 2.3 29.9 1.0
SG D:CYS188 2.4 35.4 1.0
SG D:CYS156 2.4 37.6 1.0
CB D:CYS156 3.2 37.7 1.0
CB D:CYS188 3.2 34.8 1.0
CB D:CYS153 3.3 32.0 1.0
CB D:CYS185 3.4 29.9 1.0
N D:CYS156 3.7 37.9 1.0
N D:CYS185 3.9 29.7 1.0
CA D:CYS156 3.9 37.9 1.0
N D:CYS188 4.2 34.6 1.0
CA D:CYS185 4.2 29.9 1.0
CA D:CYS188 4.3 34.8 1.0
C D:CYS156 4.6 38.1 1.0
NH2 B:ARG18 4.6 57.0 1.0
C D:GLU155 4.6 37.8 1.0
N D:PHE157 4.8 38.5 1.0
CA D:CYS153 4.8 32.0 1.0
C D:CYS185 4.9 30.3 1.0
CB D:GLU155 4.9 37.9 1.0

Zinc binding site 5 out of 8 in 1xbt

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Zinc binding site 5 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn5193

b:32.5
occ:1.00
 SG E:CYS188 2.3 35.2 1.0
SG E:CYS156 2.3 38.2 1.0
SG E:CYS153 2.3 29.4 1.0
SG E:CYS185 2.4 31.0 1.0
CB E:CYS156 3.0 37.9 1.0
CB E:CYS188 3.2 34.8 1.0
CB E:CYS153 3.3 31.4 1.0
CB E:CYS185 3.5 29.3 1.0
N E:CYS156 3.6 37.8 1.0
CA E:CYS156 3.8 38.0 1.0
N E:CYS185 3.9 29.6 1.0
CA E:CYS185 4.2 30.1 1.0
N E:CYS188 4.3 34.6 1.0
CA E:CYS188 4.4 34.8 1.0
C E:CYS156 4.5 38.1 1.0
C E:GLU155 4.6 37.6 1.0
NH2 G:ARG18 4.6 56.4 1.0
N E:PHE157 4.6 38.5 1.0
CA E:CYS153 4.7 31.8 1.0
CB E:GLU155 4.9 37.5 1.0
C E:CYS185 5.0 30.2 1.0
C E:VAL184 5.0 29.4 1.0

Zinc binding site 6 out of 8 in 1xbt

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Zinc binding site 6 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn6193

b:38.5
occ:1.00
 SG F:CYS153 2.2 31.9 1.0
SG F:CYS156 2.3 37.0 1.0
SG F:CYS185 2.3 31.7 1.0
SG F:CYS188 2.4 36.7 1.0
CB F:CYS156 3.1 37.8 1.0
CB F:CYS188 3.2 34.7 1.0
CB F:CYS153 3.3 32.0 1.0
CB F:CYS185 3.4 30.2 1.0
N F:CYS156 3.8 37.8 1.0
N F:CYS185 3.8 29.6 1.0
CA F:CYS156 4.0 37.9 1.0
NH2 H:ARG18 4.1 56.3 1.0
CA F:CYS185 4.2 30.1 1.0
N F:CYS188 4.2 34.7 1.0
CA F:CYS188 4.3 34.9 1.0
C F:CYS156 4.6 38.1 1.0
C F:GLU155 4.7 37.7 1.0
CA F:CYS153 4.8 32.0 1.0
N F:PHE157 4.8 38.5 1.0
C F:CYS185 4.9 30.3 1.0
CB F:GLU155 4.9 37.7 1.0
C F:VAL184 5.0 29.5 1.0

Zinc binding site 7 out of 8 in 1xbt

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Zinc binding site 7 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn7193

b:35.8
occ:1.00
 SG G:CYS188 2.3 36.4 1.0
SG G:CYS156 2.3 38.0 1.0
SG G:CYS185 2.3 31.5 1.0
SG G:CYS153 2.3 31.0 1.0
CB G:CYS156 3.1 37.6 1.0
CB G:CYS188 3.2 34.7 1.0
CB G:CYS153 3.3 32.0 1.0
CB G:CYS185 3.4 29.9 1.0
N G:CYS156 3.7 37.8 1.0
N G:CYS185 3.9 29.8 1.0
CA G:CYS156 3.9 37.9 1.0
NH2 E:ARG18 4.1 55.8 1.0
N G:CYS188 4.2 34.6 1.0
CA G:CYS185 4.2 30.1 1.0
CA G:CYS188 4.3 34.8 1.0
C G:CYS156 4.6 38.2 1.0
C G:GLU155 4.6 37.7 1.0
N G:PHE157 4.7 38.5 1.0
CA G:CYS153 4.8 32.0 1.0
CB G:GLU155 4.9 37.7 1.0
C G:CYS185 4.9 30.3 1.0

Zinc binding site 8 out of 8 in 1xbt

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Zinc binding site 8 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn8193

b:35.2
occ:1.00
 SG H:CYS156 2.2 37.2 1.0
SG H:CYS185 2.3 30.2 1.0
SG H:CYS153 2.3 30.2 1.0
SG H:CYS188 2.3 35.9 1.0
CB H:CYS156 3.0 37.9 1.0
CB H:CYS188 3.3 34.8 1.0
CB H:CYS153 3.3 31.4 1.0
CB H:CYS185 3.5 29.8 1.0
N H:CYS156 3.7 37.8 1.0
N H:CYS185 3.9 29.6 1.0
CA H:CYS156 3.9 37.9 1.0
CA H:CYS185 4.2 30.0 1.0
N H:CYS188 4.3 34.5 1.0
CA H:CYS188 4.4 34.9 1.0
C H:CYS156 4.5 38.2 1.0
C H:GLU155 4.6 37.8 1.0
N H:PHE157 4.7 38.5 1.0
CA H:CYS153 4.7 31.8 1.0
CB H:GLU155 4.9 37.9 1.0
C H:CYS185 4.9 30.3 1.0
NH2 F:ARG18 5.0 56.2 1.0
N H:ARG158 5.0 38.8 1.0

Reference:

M.Welin, U.Kosinska, N.E.Mikkelsen, C.Carnrot, C.Zhu, L.Wang, S.Eriksson, B.Munch-Petersen, H.Eklund. Structures of Thymidine Kinase 1 of Human and Mycoplasmic Origin Proc.Natl.Acad.Sci.Usa V. 101 17970 2004.
ISSN: ISSN 0027-8424
PubMed: 15611477
DOI: 10.1073/PNAS.0406332102
Page generated: Wed Oct 16 20:22:32 2024

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