Zinc in PDB 2qpo: Thermotoga Maritima Thymidine Kinase in the Apo Form

All present enzymatic activity of Thermotoga Maritima Thymidine Kinase in the Apo Form:
2.7.1.21;

The structure of Thermotoga Maritima Thymidine Kinase in the Apo Form, PDB code: 2qpo was solved by D.Segura-Pena, J.Lichter, M.Trani, M.Konrad, A.Lavie, S.Lutz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.61 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.600, 113.500, 54.800, 90.00, 109.16, 90.00
R / Rfree (%)	20.3 / 26.1

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

Zinc binding site 1 out of 4 in the Thermotoga Maritima Thymidine Kinase in the Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermotoga Maritima Thymidine Kinase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:19.1 occ:1.00 SG A:CYS140 2.2 14.1 1.0 SG A:CYS176 2.4 14.9 1.0 SG A:CYS143 2.4 18.9 1.0 SG A:CYS173 2.4 14.7 1.0 CB A:CYS140 3.1 14.5 1.0 CB A:CYS176 3.2 14.3 1.0 CB A:CYS143 3.3 18.3 1.0 CB A:CYS173 3.5 13.1 1.0 N A:CYS143 3.8 18.1 1.0 N A:CYS173 3.8 12.9 1.0 CA A:CYS143 4.1 18.6 1.0 OD1 A:ASN147 4.2 16.2 1.0 CA A:CYS173 4.2 12.8 1.0 O A:HOH336 4.4 17.7 1.0 CA A:CYS176 4.4 14.1 1.0 N A:CYS176 4.4 13.5 1.0 CA A:CYS140 4.5 14.3 1.0 ND2 A:ASN147 4.7 18.2 1.0 CB A:ARG142 4.7 17.4 1.0 CG A:ASN147 4.9 17.4 1.0 C A:ARG142 4.9 18.1 1.0 C A:CYS143 4.9 19.5 1.0 C A:CYS173 4.9 13.1 1.0 C A:VAL172 4.9 13.0 1.0 O A:CYS173 4.9 13.1 1.0

Zinc binding site 2 out of 4 in the Thermotoga Maritima Thymidine Kinase in the Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermotoga Maritima Thymidine Kinase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:24.6 occ:1.00 SG B:CYS140 2.2 21.8 1.0 SG B:CYS143 2.3 21.7 1.0 SG B:CYS173 2.4 20.9 1.0 SG B:CYS176 2.5 22.2 1.0 CB B:CYS140 3.2 21.1 1.0 CB B:CYS143 3.2 22.9 1.0 CB B:CYS176 3.4 22.2 1.0 CB B:CYS173 3.7 19.0 1.0 N B:CYS143 3.7 23.5 1.0 N B:CYS173 3.9 19.1 1.0 CA B:CYS143 4.0 23.1 1.0 OD1 B:ASN147 4.3 19.0 1.0 CA B:CYS173 4.4 19.5 1.0 ND2 B:ASN147 4.4 19.3 1.0 O B:HOH317 4.4 22.0 1.0 N B:CYS176 4.4 22.6 1.0 CA B:CYS176 4.5 22.3 1.0 CA B:CYS140 4.6 21.6 1.0 C B:CYS143 4.7 23.3 1.0 CG B:ASN147 4.8 20.4 1.0 C B:ARG142 4.8 24.0 1.0 CB B:ARG142 4.8 24.3 1.0 O B:CYS173 5.0 20.9 1.0

Zinc binding site 3 out of 4 in the Thermotoga Maritima Thymidine Kinase in the Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermotoga Maritima Thymidine Kinase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn204 b:20.6 occ:1.00 SG C:CYS143 2.3 16.6 1.0 SG C:CYS140 2.3 15.6 1.0 SG C:CYS173 2.3 14.8 1.0 SG C:CYS176 2.5 19.4 1.0 CB C:CYS140 3.2 16.4 1.0 CB C:CYS176 3.2 19.5 1.0 CB C:CYS143 3.3 19.8 1.0 CB C:CYS173 3.5 15.4 1.0 N C:CYS143 3.8 19.4 1.0 N C:CYS173 3.9 16.9 1.0 CA C:CYS143 4.1 19.5 1.0 OD1 C:ASN147 4.2 21.8 1.0 CA C:CYS173 4.3 15.5 1.0 N C:CYS176 4.4 18.1 1.0 CA C:CYS176 4.4 18.6 1.0 ND2 C:ASN147 4.6 21.5 1.0 CA C:CYS140 4.6 16.7 1.0 CB C:ARG142 4.8 20.9 1.0 CG C:ASN147 4.8 20.6 1.0 C C:ARG142 4.9 20.5 1.0 C C:CYS143 4.9 19.4 1.0 C C:CYS173 5.0 15.5 1.0 O C:CYS173 5.0 14.5 1.0

Zinc binding site 4 out of 4 in the Thermotoga Maritima Thymidine Kinase in the Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermotoga Maritima Thymidine Kinase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:24.9 occ:1.00 SG D:CYS140 2.3 23.6 1.0 SG D:CYS173 2.3 18.3 1.0 CB D:CYS143 2.4 25.6 1.0 SG D:CYS176 2.4 20.5 1.0 SG D:CYS143 2.5 26.5 1.0 CB D:CYS140 3.3 20.0 1.0 CB D:CYS176 3.4 21.4 1.0 CB D:CYS173 3.5 19.4 1.0 CA D:CYS143 3.6 25.1 1.0 N D:CYS173 3.9 19.2 1.0 N D:CYS143 3.9 24.3 1.0 OD1 D:ASN147 4.2 21.1 1.0 CA D:CYS173 4.3 18.6 1.0 N D:CYS176 4.4 22.1 1.0 CA D:CYS176 4.5 21.9 1.0 O D:HOH340 4.5 22.0 1.0 ND2 D:ASN147 4.6 21.5 1.0 CA D:CYS140 4.7 21.0 1.0 C D:CYS143 4.8 25.3 1.0 CG D:ASN147 4.8 19.9 1.0 C D:CYS173 4.9 18.4 1.0 O D:CYS173 4.9 17.6 1.0 C D:ARG142 5.0 23.6 1.0 CB D:ARG142 5.0 22.6 1.0

D.Segura-Pena, J.Lichter, M.Trani, M.Konrad, A.Lavie, S.Lutz. Quaternary Structure Change As A Mechanism For the Regulation of Thymidine Kinase 1-Like Enzymes. Structure V. 15 1555 2007.
ISSN: ISSN 0969-2126
PubMed: 18073106
DOI: 10.1016/J.STR.2007.09.025