Zinc in PDB 9k6k: Monkeypox Thymidine Kinase

All present enzymatic activity of Monkeypox Thymidine Kinase:
2.7.1.21;

The structure of Monkeypox Thymidine Kinase, PDB code: 9k6k was solved by T.Zhang, W.Cui, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.88 / 2.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.272, 63.762, 117.106, 90, 111.16, 90
R / Rfree (%)	22.5 / 26.4

The binding sites of Zinc atom in the Monkeypox Thymidine Kinase (pdb code 9k6k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Monkeypox Thymidine Kinase, PDB code: 9k6k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Monkeypox Thymidine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Monkeypox Thymidine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:83.0 occ:1.00 SG A:CYS141 2.1 99.6 1.0 SG A:CYS173 2.3 86.1 1.0 SG A:CYS170 2.5 73.0 1.0 SG A:CYS138 2.6 88.0 1.0 CB A:CYS141 3.3 108.5 1.0 CB A:CYS173 3.4 81.3 1.0 CB A:CYS138 3.5 83.5 1.0 N A:CYS141 3.6 94.7 1.0 CB A:CYS170 3.8 70.8 1.0 CA A:CYS141 4.0 97.2 1.0 CG A:LYS143 4.3 107.7 1.0 N A:CYS173 4.4 89.2 1.0 N A:CYS170 4.4 81.8 1.0 CD A:LYS143 4.5 120.4 1.0 CA A:CYS173 4.5 83.3 1.0 C A:CYS141 4.5 92.1 1.0 CB A:LYS140 4.6 103.1 1.0 CE A:LYS172 4.7 101.8 1.0 CA A:CYS170 4.7 73.6 1.0 C A:LYS140 4.7 98.0 1.0 N A:PHE142 4.9 88.9 1.0 CA A:CYS138 4.9 81.4 1.0 CA A:LYS140 5.0 99.6 1.0 N A:LYS140 5.0 92.9 1.0

Zinc binding site 2 out of 4 in the Monkeypox Thymidine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Monkeypox Thymidine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:112.2 occ:1.00 SG B:CYS141 2.2 71.4 1.0 SG B:CYS170 2.3 80.0 1.0 SG B:CYS173 2.5 98.1 1.0 SG B:CYS138 2.6 87.4 1.0 CB B:CYS141 3.2 80.5 1.0 CB B:CYS173 3.3 92.8 1.0 CB B:CYS170 3.6 75.6 1.0 CB B:CYS138 3.6 82.8 1.0 N B:CYS141 3.8 96.0 1.0 N B:CYS170 4.0 83.6 1.0 CA B:CYS141 4.0 88.0 1.0 N B:CYS173 4.3 100.5 1.0 CA B:CYS170 4.4 78.7 1.0 CA B:CYS173 4.4 94.1 1.0 C B:CYS141 4.7 92.2 1.0 CB B:LYS140 4.7 99.2 1.0 C B:LYS140 4.8 96.6 1.0 C B:CYS170 4.9 78.9 1.0

Zinc binding site 3 out of 4 in the Monkeypox Thymidine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Monkeypox Thymidine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:113.1 occ:1.00 SG C:CYS141 2.3 105.1 1.0 SG C:CYS138 2.4 99.2 1.0 SG C:CYS173 2.4 114.1 1.0 SG C:CYS170 2.8 110.7 1.0 CB C:CYS141 3.3 108.1 1.0 CB C:CYS138 3.4 90.5 1.0 CB C:CYS173 3.4 106.6 1.0 N C:CYS141 3.5 92.2 1.0 CA C:CYS141 3.9 100.4 1.0 CB C:CYS170 4.0 103.7 1.0 N C:CYS170 4.2 105.4 1.0 CB C:LYS140 4.4 89.2 1.0 C C:CYS141 4.5 97.9 1.0 C C:LYS140 4.5 95.3 1.0 N C:CYS173 4.5 97.8 1.0 CA C:CYS173 4.6 101.8 1.0 CA C:CYS170 4.7 100.6 1.0 CA C:CYS138 4.8 86.5 1.0 CB C:LYS143 4.8 105.1 1.0 CA C:LYS140 4.8 92.4 1.0 N C:LYS140 4.8 88.6 1.0 N C:PHE142 4.9 96.7 1.0 N C:LYS143 4.9 107.9 1.0

Zinc binding site 4 out of 4 in the Monkeypox Thymidine Kinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Monkeypox Thymidine Kinase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:125.5 occ:1.00 SG D:CYS141 2.0 114.0 1.0 SG D:CYS138 2.3 82.5 1.0 SG D:CYS170 2.3 110.2 1.0 SG D:CYS173 2.4 105.9 1.0 CB D:CYS173 3.1 103.6 1.0 CB D:CYS141 3.3 101.5 1.0 CB D:CYS138 3.4 83.9 1.0 CB D:CYS170 3.5 100.0 1.0 N D:CYS170 3.6 98.1 1.0 N D:CYS141 3.8 85.5 1.0 N D:CYS173 4.0 101.1 1.0 CA D:CYS170 4.1 91.7 1.0 CA D:CYS141 4.1 92.7 1.0 CA D:CYS173 4.2 103.9 1.0 C D:CYS141 4.6 83.4 1.0 C D:VAL169 4.7 93.1 1.0 C D:CYS170 4.7 86.8 1.0 CA D:VAL169 4.8 89.9 1.0 CB D:VAL169 4.8 95.7 1.0 CB D:LYS140 4.8 95.2 1.0 CA D:CYS138 4.8 83.0 1.0 C D:LYS140 4.9 95.9 1.0 O D:CYS170 5.0 88.3 1.0

T.Zhang, X.Chen, C.Tao, H.Huang, Z.Luo, M.Liu, W.Cui, W.Wang. Structural and Mechanistic Insight Into the Phosphorylation Reaction Catalyzed By Mpox Virus Thymidine Kinase. Antiviral Res. V. 237 06125 2025.
ISSN: ISSN 0166-3542
PubMed: 40020877
DOI: 10.1016/J.ANTIVIRAL.2025.106125