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Zinc in PDB 5fuy: Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp

Enzymatic activity of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp

All present enzymatic activity of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp:
2.7.1.21;

Protein crystallography data

The structure of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp, PDB code: 5fuy was solved by J.Timm, M.Valente, V.Castillo-Acosta, T.Balzarini, J.E.Nettleship, H.Rada, K.S.Wilson, D.Gonzalez-Pacanowska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 152.22 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.614, 96.999, 304.431, 90.00, 90.00, 90.00
R / Rfree (%) 20.847 / 24.344

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp (pdb code 5fuy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp, PDB code: 5fuy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5fuy

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Zinc binding site 1 out of 6 in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1387

b:58.6
occ:1.00
 SG A:CYS377 2.3 62.8 1.0
SG A:CYS344 2.3 69.0 1.0
SG A:CYS341 2.3 55.3 1.0
SG A:CYS374 2.4 60.1 1.0
CB A:CYS344 3.2 72.3 1.0
CB A:CYS341 3.2 58.9 1.0
CB A:CYS377 3.3 63.9 1.0
CB A:CYS374 3.5 55.1 1.0
N A:CYS344 3.8 76.8 1.0
N A:CYS374 4.0 52.8 1.0
CA A:CYS344 4.0 74.5 1.0
CA A:CYS374 4.3 55.7 1.0
N A:CYS377 4.4 67.2 1.0
CA A:CYS377 4.4 66.0 1.0
CD A:ARG347 4.6 94.9 1.0
CA A:CYS341 4.7 62.4 1.0
NH1 A:ARG347 4.7 0.3 1.0
CB A:GLU343 4.8 82.1 1.0
C A:CYS344 4.9 76.1 1.0
C A:GLU343 4.9 74.9 1.0
CB A:ARG347 4.9 93.0 1.0
N A:HIS345 4.9 80.4 1.0
C A:CYS374 5.0 56.1 1.0

Zinc binding site 2 out of 6 in 5fuy

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Zinc binding site 2 out of 6 in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1386

b:72.5
occ:1.00
 SG B:CYS344 2.3 78.7 1.0
SG B:CYS377 2.3 77.6 1.0
SG B:CYS374 2.3 75.2 1.0
SG B:CYS341 2.4 64.7 1.0
CB B:CYS344 3.2 82.3 1.0
CB B:CYS341 3.3 71.8 1.0
CB B:CYS377 3.4 77.8 1.0
CB B:CYS374 3.5 70.8 1.0
N B:CYS344 3.8 81.4 1.0
N B:CYS374 4.0 62.9 1.0
CA B:CYS344 4.1 83.3 1.0
CA B:CYS374 4.3 68.0 1.0
N B:CYS377 4.4 79.3 1.0
CD B:ARG347 4.5 0.9 1.0
CA B:CYS377 4.5 78.7 1.0
CA B:CYS341 4.7 70.2 1.0
CB B:GLU343 4.8 90.2 1.0
CB B:ARG347 4.8 93.5 1.0
C B:CYS344 4.9 85.6 1.0
C B:GLU343 5.0 83.5 1.0
CG B:ARG347 5.0 99.9 1.0
N B:HIS345 5.0 91.0 1.0
C B:CYS374 5.0 68.5 1.0

Zinc binding site 3 out of 6 in 5fuy

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Zinc binding site 3 out of 6 in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1387

b:83.8
occ:1.00
 SG C:CYS341 2.3 65.5 1.0
SG C:CYS377 2.3 81.1 1.0
SG C:CYS344 2.3 84.0 1.0
SG C:CYS374 2.4 82.9 1.0
CB C:CYS341 3.2 70.1 1.0
CB C:CYS344 3.2 89.2 1.0
CB C:CYS377 3.3 86.6 1.0
CB C:CYS374 3.5 76.6 1.0
N C:CYS344 3.8 86.3 1.0
N C:CYS374 4.0 73.0 1.0
CA C:CYS344 4.1 89.6 1.0
CA C:CYS374 4.3 74.2 1.0
CA C:CYS377 4.4 85.9 1.0
N C:CYS377 4.4 77.8 1.0
CD C:ARG347 4.5 99.8 1.0
CA C:CYS341 4.6 68.5 1.0
CB C:GLU343 4.8 90.9 1.0
CB C:ARG347 4.9 97.8 1.0
C C:CYS344 4.9 89.6 1.0
C C:GLU343 4.9 88.1 1.0
C C:CYS374 5.0 73.7 1.0
N C:HIS345 5.0 88.4 1.0
CG C:ARG347 5.0 98.2 1.0

Zinc binding site 4 out of 6 in 5fuy

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Zinc binding site 4 out of 6 in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1385

b:86.8
occ:1.00
 SG D:CYS344 2.3 0.0 1.0
SG D:CYS341 2.3 94.0 1.0
SG D:CYS374 2.3 91.7 1.0
SG D:CYS377 2.3 86.2 1.0
CB D:CYS341 3.2 91.0 1.0
CB D:CYS344 3.2 97.6 1.0
CB D:CYS377 3.4 85.0 1.0
CB D:CYS374 3.5 96.5 1.0
N D:CYS344 3.8 0.4 1.0
N D:CYS374 4.0 89.7 1.0
CA D:CYS344 4.1 97.9 1.0
CA D:CYS374 4.3 93.7 1.0
N D:CYS377 4.5 87.2 1.0
CA D:CYS377 4.5 85.9 1.0
CA D:CYS341 4.7 89.3 1.0
CB D:ARG347 4.7 73.3 1.0
CB D:GLU343 4.8 0.4 1.0
C D:CYS344 4.9 89.4 1.0
C D:CYS374 5.0 89.9 1.0
C D:GLU343 5.0 0.0 1.0

Zinc binding site 5 out of 6 in 5fuy

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Zinc binding site 5 out of 6 in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1388

b:56.2
occ:1.00
 SG E:CYS377 2.3 66.5 1.0
SG E:CYS344 2.3 69.3 1.0
SG E:CYS341 2.3 48.4 1.0
SG E:CYS374 2.3 55.3 1.0
CB E:CYS344 3.2 63.2 1.0
CB E:CYS341 3.3 49.8 1.0
CB E:CYS377 3.3 66.8 1.0
CB E:CYS374 3.5 53.5 1.0
N E:CYS344 3.8 69.5 1.0
N E:CYS374 4.0 51.1 1.0
CA E:CYS344 4.1 66.4 1.0
CA E:CYS374 4.3 53.5 1.0
N E:CYS377 4.4 71.7 1.0
CA E:CYS377 4.5 66.0 1.0
CD E:ARG347 4.5 87.7 1.0
CA E:CYS341 4.7 54.4 1.0
CB E:GLU343 4.8 70.5 1.0
C E:CYS344 4.9 70.6 1.0
CB E:ARG347 4.9 70.7 1.0
C E:GLU343 4.9 68.1 1.0
N E:HIS345 4.9 79.4 1.0
C E:CYS374 4.9 54.3 1.0
CG E:ARG347 5.0 81.0 1.0
NE E:ARG347 5.0 0.2 1.0

Zinc binding site 6 out of 6 in 5fuy

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Zinc binding site 6 out of 6 in the Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Domain of Thymidine Kinase From Trypanosoma Brucei with Dtmp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1387

b:58.5
occ:1.00
 SG F:CYS377 2.3 59.8 1.0
SG F:CYS344 2.3 64.5 1.0
SG F:CYS341 2.3 54.5 1.0
SG F:CYS374 2.4 54.9 1.0
CB F:CYS344 3.2 67.7 1.0
CB F:CYS341 3.2 57.7 1.0
CB F:CYS377 3.3 60.1 1.0
CB F:CYS374 3.5 52.3 1.0
N F:CYS344 3.8 67.2 1.0
N F:CYS374 4.0 48.7 1.0
CA F:CYS344 4.1 68.0 1.0
CA F:CYS374 4.3 49.8 1.0
N F:CYS377 4.4 67.5 1.0
CA F:CYS377 4.4 62.0 1.0
CA F:CYS341 4.7 57.8 1.0
CD F:ARG347 4.7 85.4 1.0
CB F:GLU343 4.8 70.4 1.0
C F:CYS344 4.9 73.9 1.0
CB F:ARG347 4.9 74.2 1.0
C F:GLU343 4.9 67.6 1.0
N F:HIS345 4.9 77.2 1.0
C F:CYS374 5.0 53.2 1.0

Reference:

M.Valente, J.Timm, V.M.Castillo-Acosta, L.M.Ruiz-Perez, T.Balzarini, J.E.Nettleship, L.E.Bird, H.Rada, K.S.Wilson, D.Gonzalez-Pacanowska. Cell Cycle Regulation and Novel Structural Features of Thymidine Kinase, An Essential Enzyme in Trypanosoma Brucei. Mol.Microbiol. V. 102 365 2016.
ISSN: ISSN 0950-382X
PubMed: 27426054
DOI: 10.1111/MMI.13467
Page generated: Wed Dec 16 06:16:41 2020

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