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Zinc in PDB 1w4r: Structure of A Type II Thymidine Kinase with Bound Dttp

Enzymatic activity of Structure of A Type II Thymidine Kinase with Bound Dttp

All present enzymatic activity of Structure of A Type II Thymidine Kinase with Bound Dttp:
2.7.1.21;

Protein crystallography data

The structure of Structure of A Type II Thymidine Kinase with Bound Dttp, PDB code: 1w4r was solved by M.S.Birringer, M.T.Claus, G.Folkers, D.P.Kloer, G.E.Schulz, L.Scapozza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.496, 122.920, 115.274, 90.00, 130.00, 90.00
R / Rfree (%) 15.9 / 18.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Type II Thymidine Kinase with Bound Dttp (pdb code 1w4r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of A Type II Thymidine Kinase with Bound Dttp, PDB code: 1w4r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1w4r

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Zinc binding site 1 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:25.9
occ:1.00
 SG A:CYS156 2.3 27.4 1.0
SG A:CYS185 2.3 25.0 1.0
SG A:CYS188 2.3 28.4 1.0
SG A:CYS153 2.4 21.9 1.0
CB A:CYS156 3.1 28.0 1.0
CB A:CYS188 3.3 25.2 1.0
CB A:CYS153 3.3 21.6 1.0
CB A:CYS185 3.5 22.5 1.0
N A:CYS156 3.7 28.3 1.0
N A:CYS185 3.9 20.6 1.0
CA A:CYS156 3.9 28.0 1.0
N A:CYS188 4.2 25.6 1.0
CA A:CYS185 4.3 21.3 1.0
CA A:CYS188 4.3 26.0 1.0
C A:CYS156 4.6 28.8 1.0
C A:GLU155 4.6 28.9 1.0
N A:PHE157 4.7 29.2 1.0
O A:HOH2033 4.7 38.1 1.0
CA A:CYS153 4.7 21.7 1.0
CB A:GLU155 4.9 27.8 1.0
C A:CYS185 4.9 21.3 1.0
O A:CYS185 4.9 21.3 1.0

Zinc binding site 2 out of 8 in 1w4r

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Zinc binding site 2 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:28.1
occ:1.00
 SG B:CYS156 2.3 28.3 1.0
SG B:CYS185 2.3 26.6 1.0
SG B:CYS153 2.3 24.2 1.0
SG B:CYS188 2.3 27.9 1.0
CB B:CYS188 3.2 27.7 1.0
CB B:CYS156 3.2 29.3 1.0
CB B:CYS153 3.3 23.9 1.0
CB B:CYS185 3.5 24.0 1.0
N B:CYS156 3.7 29.5 1.0
N B:CYS185 3.9 23.1 1.0
CA B:CYS156 4.0 29.5 1.0
N B:CYS188 4.2 28.4 1.0
CA B:CYS188 4.3 28.1 1.0
CA B:CYS185 4.3 24.0 1.0
C B:CYS156 4.5 30.1 1.0
C B:GLU155 4.6 30.6 1.0
NE B:ARG158 4.6 38.9 0.5
N B:PHE157 4.6 30.4 1.0
CA B:CYS153 4.7 23.3 1.0
CB B:GLU155 4.8 30.2 1.0
NH2 B:ARG158 4.9 34.0 0.5
C B:CYS185 4.9 24.1 1.0
CB B:ARG158 4.9 30.6 0.5
N B:ARG158 5.0 30.9 0.5
O B:CYS185 5.0 22.8 1.0
N B:ARG158 5.0 31.0 0.5

Zinc binding site 3 out of 8 in 1w4r

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Zinc binding site 3 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:27.9
occ:1.00
 SG C:CYS153 2.3 26.6 1.0
SG C:CYS156 2.3 29.3 1.0
SG C:CYS188 2.3 31.4 1.0
SG C:CYS185 2.4 25.6 1.0
CB C:CYS188 3.2 29.7 1.0
CB C:CYS156 3.2 30.3 1.0
CB C:CYS153 3.3 24.6 1.0
CB C:CYS185 3.6 25.5 1.0
N C:CYS156 3.7 30.7 1.0
N C:CYS185 3.9 24.6 1.0
CA C:CYS156 4.0 29.8 1.0
N C:CYS188 4.2 29.8 1.0
CA C:CYS188 4.3 30.5 1.0
CA C:CYS185 4.3 23.8 1.0
C C:GLU155 4.6 31.6 1.0
C C:CYS156 4.6 30.2 1.0
N C:PHE157 4.7 30.6 1.0
CA C:CYS153 4.8 25.3 1.0
NH2 B:ARG18 4.8 59.9 1.0
CB C:GLU155 4.9 31.5 1.0
C C:CYS185 4.9 23.7 1.0
N C:ARG158 5.0 30.4 1.0
O C:CYS185 5.0 23.3 1.0

Zinc binding site 4 out of 8 in 1w4r

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Zinc binding site 4 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn400

b:26.1
occ:1.00
 SG D:CYS156 2.3 28.5 1.0
SG D:CYS188 2.3 25.2 1.0
SG D:CYS153 2.3 24.1 1.0
SG D:CYS185 2.4 23.3 1.0
CB D:CYS156 3.1 29.9 1.0
CB D:CYS188 3.2 23.6 1.0
CB D:CYS153 3.3 22.5 1.0
CB D:CYS185 3.6 21.9 1.0
N D:CYS156 3.6 30.6 1.0
CA D:CYS156 3.9 29.8 1.0
N D:CYS185 3.9 22.3 1.0
N D:CYS188 4.2 23.9 1.0
CA D:CYS188 4.3 24.1 1.0
CA D:CYS185 4.3 21.7 1.0
C D:GLU155 4.5 30.4 1.0
C D:CYS156 4.5 29.8 1.0
N D:PHE157 4.7 31.0 1.0
CA D:CYS153 4.8 23.2 1.0
C D:CYS185 4.9 21.2 1.0
CB D:GLU155 4.9 29.3 1.0
CA D:GLU155 5.0 29.7 1.0
O D:CYS185 5.0 20.2 1.0

Zinc binding site 5 out of 8 in 1w4r

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Zinc binding site 5 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn400

b:33.6
occ:1.00
 SG E:CYS156 2.3 35.0 1.0
SG E:CYS153 2.3 32.1 1.0
SG E:CYS185 2.4 32.4 1.0
SG E:CYS188 2.4 34.4 1.0
CB E:CYS156 3.2 38.2 1.0
CB E:CYS188 3.2 34.8 1.0
CB E:CYS153 3.3 30.1 1.0
CB E:CYS185 3.5 30.6 1.0
N E:CYS156 3.6 38.5 1.0
N E:CYS185 3.9 28.9 1.0
CA E:CYS156 3.9 38.0 1.0
N E:CYS188 4.2 35.5 1.0
CA E:CYS185 4.3 30.0 1.0
CA E:CYS188 4.3 35.3 1.0
C E:CYS156 4.5 38.8 1.0
C E:GLU155 4.5 38.8 1.0
N E:PHE157 4.5 39.4 1.0
O E:HOH2062 4.7 45.8 1.0
CA E:CYS153 4.7 30.7 1.0
CB E:GLU155 4.8 38.0 1.0
C E:CYS185 4.9 30.1 1.0
N E:ARG158 4.9 38.0 1.0
CB E:ARG158 5.0 38.1 1.0
O E:CYS185 5.0 30.6 1.0
C E:VAL184 5.0 28.6 1.0

Zinc binding site 6 out of 8 in 1w4r

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Zinc binding site 6 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn400

b:27.8
occ:1.00
 SG F:CYS153 2.3 24.8 1.0
SG F:CYS188 2.3 30.2 1.0
SG F:CYS156 2.3 28.5 1.0
SG F:CYS185 2.4 25.1 1.0
CB F:CYS156 3.2 30.0 1.0
CB F:CYS188 3.2 28.1 1.0
CB F:CYS153 3.3 24.5 1.0
CB F:CYS185 3.6 24.5 1.0
N F:CYS156 3.7 30.4 1.0
N F:CYS185 3.9 23.3 1.0
CA F:CYS156 3.9 30.4 1.0
N F:CYS188 4.2 28.1 1.0
CA F:CYS185 4.3 23.1 1.0
CA F:CYS188 4.3 28.3 1.0
C F:GLU155 4.5 31.1 1.0
C F:CYS156 4.6 30.4 1.0
N F:PHE157 4.7 30.6 1.0
CA F:CYS153 4.7 24.4 1.0
CB F:GLU155 4.8 30.6 1.0
NH1 F:ARG158 4.9 39.2 0.5
C F:CYS185 4.9 23.2 1.0
O F:CYS185 4.9 24.0 1.0
CA F:GLU155 5.0 30.7 1.0
CB F:ARG158 5.0 29.4 0.5
C F:VAL184 5.0 22.1 1.0

Zinc binding site 7 out of 8 in 1w4r

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Zinc binding site 7 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn400

b:25.1
occ:1.00
 SG G:CYS156 2.3 26.8 1.0
SG G:CYS153 2.3 23.2 1.0
SG G:CYS188 2.3 27.1 1.0
SG G:CYS185 2.4 22.9 1.0
CB G:CYS156 3.2 28.8 1.0
CB G:CYS188 3.2 24.0 1.0
CB G:CYS153 3.3 22.9 1.0
CB G:CYS185 3.6 21.1 1.0
N G:CYS156 3.7 28.3 1.0
N G:CYS185 3.9 21.7 1.0
CA G:CYS156 4.0 29.2 1.0
N G:CYS188 4.2 24.1 1.0
CA G:CYS185 4.3 21.0 1.0
CA G:CYS188 4.3 24.2 1.0
C G:GLU155 4.6 28.7 1.0
C G:CYS156 4.6 29.6 1.0
N G:PHE157 4.7 30.6 1.0
CA G:CYS153 4.7 22.2 1.0
CB G:GLU155 4.8 28.2 1.0
C G:CYS185 4.8 20.7 1.0
O G:CYS185 4.9 19.9 1.0
C G:VAL184 5.0 20.6 1.0
N G:ARG158 5.0 31.1 1.0

Zinc binding site 8 out of 8 in 1w4r

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Zinc binding site 8 out of 8 in the Structure of A Type II Thymidine Kinase with Bound Dttp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Type II Thymidine Kinase with Bound Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn400

b:26.4
occ:1.00
 SG H:CYS153 2.3 25.5 1.0
SG H:CYS156 2.3 28.3 1.0
SG H:CYS185 2.3 25.1 1.0
SG H:CYS188 2.4 27.1 1.0
CB H:CYS156 3.2 28.7 1.0
CB H:CYS188 3.2 27.2 1.0
CB H:CYS153 3.3 23.3 1.0
CB H:CYS185 3.5 23.4 1.0
N H:CYS156 3.7 27.8 1.0
N H:CYS185 3.9 22.1 1.0
CA H:CYS156 4.0 28.7 1.0
N H:CYS188 4.2 27.1 1.0
CA H:CYS185 4.3 22.5 1.0
CA H:CYS188 4.3 26.9 1.0
NH2 E:ARG18 4.3 55.0 1.0
C H:CYS156 4.6 29.9 1.0
C H:GLU155 4.6 29.1 1.0
N H:PHE157 4.7 30.2 1.0
CA H:CYS153 4.7 23.1 1.0
NH1 E:ARG18 4.8 51.5 1.0
C H:CYS185 4.9 22.7 1.0
O H:CYS185 4.9 22.6 1.0
CB H:GLU155 4.9 29.1 1.0
N H:ARG158 5.0 30.7 1.0

Reference:

M.S.Birringer, M.T.Claus, G.Folkers, D.P.Kloer, G.E.Schulz, L.Scapozza. Structure of A Type II Thymidine Kinase with Bound Dttp Febs Lett. V. 579 1376 2005.
ISSN: ISSN 0014-5793
PubMed: 15733844
DOI: 10.1016/J.FEBSLET.2005.01.034
Page generated: Mon Jan 25 16:15:18 2021

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