Zinc in PDB 2b8t: Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine

All present enzymatic activity of Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine:
2.7.1.21;

The structure of Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine, PDB code: 2b8t was solved by U.Kosinska, C.Carnrot, S.Eriksson, L.Wang, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.95 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.158, 115.649, 64.474, 90.00, 101.02, 90.00
R / Rfree (%)	19.5 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine (pdb code 2b8t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine, PDB code: 2b8t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine


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 Thymidine Kinase From U.Urealyticum in Complex with Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1218 b:33.4 occ:1.00 ND1 A:HIS194 2.1 37.2 1.0 SG A:CYS191 2.3 31.0 1.0 SG A:CYS153 2.4 31.4 1.0 SG A:CYS156 2.4 35.7 1.0 CE1 A:HIS194 2.9 39.8 1.0 CG A:HIS194 3.2 37.6 1.0 CB A:CYS153 3.3 30.3 1.0 CB A:CYS156 3.4 39.3 1.0 CB A:CYS191 3.6 27.7 1.0 CB A:HIS194 3.7 34.9 1.0 N A:CYS156 3.8 38.4 1.0 N A:CYS191 4.0 26.0 1.0 NE2 A:HIS194 4.1 42.2 1.0 CA A:CYS156 4.1 39.2 1.0 CD2 A:HIS194 4.3 40.5 1.0 CA A:CYS191 4.4 26.2 1.0 CB A:GLU155 4.6 40.8 1.0 N A:HIS194 4.6 34.1 1.0 C A:GLU155 4.7 40.9 1.0 CA A:CYS153 4.8 29.7 1.0 CA A:HIS194 4.8 34.8 1.0 C A:CYS156 4.8 38.0 1.0 N A:GLY157 4.9 36.0 1.0 CB A:ALA158 4.9 32.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine


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 Thymidine Kinase From U.Urealyticum in Complex with Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2218 b:37.7 occ:1.00 ND1 B:HIS194 2.1 39.6 1.0 SG B:CYS153 2.3 32.0 1.0 SG B:CYS156 2.4 37.3 1.0 SG B:CYS191 2.4 33.4 1.0 CE1 B:HIS194 3.0 43.0 1.0 CB B:CYS153 3.2 30.8 1.0 CG B:HIS194 3.3 39.9 1.0 CB B:CYS156 3.5 41.4 1.0 CB B:CYS191 3.6 29.3 1.0 CB B:HIS194 3.7 36.9 1.0 N B:CYS156 3.8 40.2 1.0 N B:CYS191 3.9 27.4 1.0 NE2 B:HIS194 4.1 45.1 1.0 CA B:CYS156 4.1 41.3 1.0 CD2 B:HIS194 4.3 43.4 1.0 CA B:CYS191 4.4 27.7 1.0 CB B:GLU155 4.5 42.6 1.0 N B:HIS194 4.6 36.0 1.0 C B:GLU155 4.6 42.9 1.0 CA B:CYS153 4.7 30.1 1.0 CB B:ALA158 4.8 34.3 1.0 CA B:HIS194 4.8 37.0 1.0 C B:CYS156 4.8 39.9 1.0 CA B:GLU155 4.9 42.2 1.0 N B:GLY157 4.9 37.6 1.0 N B:GLU155 4.9 39.1 1.0 C B:CYS191 5.0 28.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine


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 Thymidine Kinase From U.Urealyticum in Complex with Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3218 b:29.8 occ:1.00 ND1 C:HIS194 2.1 32.1 1.0 SG C:CYS156 2.2 29.8 1.0 SG C:CYS153 2.3 27.2 1.0 SG C:CYS191 2.4 26.2 1.0 CE1 C:HIS194 3.0 34.1 1.0 CB C:CYS153 3.2 25.7 1.0 CG C:HIS194 3.3 32.1 1.0 CB C:CYS156 3.4 33.5 1.0 CB C:CYS191 3.5 23.2 1.0 CB C:HIS194 3.7 30.3 1.0 N C:CYS156 3.7 32.8 1.0 N C:CYS191 3.9 22.2 1.0 CA C:CYS156 4.1 33.5 1.0 NE2 C:HIS194 4.1 35.9 1.0 CD2 C:HIS194 4.3 34.3 1.0 CA C:CYS191 4.3 22.2 1.0 CB C:GLU155 4.4 35.0 1.0 CA C:CYS153 4.7 25.5 1.0 C C:GLU155 4.7 35.1 1.0 N C:HIS194 4.7 29.6 1.0 CB C:ALA158 4.8 28.2 1.0 C C:CYS156 4.8 32.6 1.0 N C:GLY157 4.8 30.5 1.0 CA C:HIS194 4.9 30.5 1.0 CA C:GLU155 4.9 34.8 1.0 N C:GLU155 5.0 32.2 1.0 C C:CYS191 5.0 22.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Thymidine Kinase From U.Urealyticum in Complex with Thymidine


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 Thymidine Kinase From U.Urealyticum in Complex with Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4218 b:32.3 occ:1.00 ND1 D:HIS194 2.1 38.6 1.0 SG D:CYS153 2.3 34.0 1.0 SG D:CYS191 2.3 32.1 1.0 SG D:CYS156 2.4 35.5 1.0 CE1 D:HIS194 3.0 41.2 1.0 CG D:HIS194 3.2 40.4 1.0 CB D:CYS153 3.3 31.5 1.0 CB D:CYS156 3.5 41.0 1.0 CB D:CYS191 3.5 28.8 1.0 CB D:HIS194 3.5 38.1 1.0 N D:CYS156 3.8 40.4 1.0 N D:CYS191 3.9 27.7 1.0 NE2 D:HIS194 4.2 45.3 1.0 CA D:CYS156 4.2 41.0 1.0 CD2 D:HIS194 4.3 44.0 1.0 CA D:CYS191 4.3 27.6 1.0 CB D:GLU155 4.4 43.7 1.0 N D:HIS194 4.6 37.8 1.0 CA D:CYS153 4.7 31.0 1.0 C D:GLU155 4.7 43.6 1.0 CA D:HIS194 4.7 38.9 1.0 CB D:ALA158 4.9 33.5 1.0 C D:CYS156 4.9 39.3 1.0 CA D:GLU155 4.9 43.4 1.0 C D:CYS191 5.0 28.7 1.0

U.Kosinska, C.Carnrot, S.Eriksson, L.Wang, H.Eklund. Structure of the Substrate Complex of Thymidine Kinase From Ureaplasma Urealyticum and Investigations of Possible Drug Targets For the Enzyme Febs Lett. V. 272 6365 2005.
ISSN: ISSN 0014-5793
PubMed: 16336273
DOI: 10.1111/J.1742-4658.2005.05030.X