Zinc in PDB 2uz3: Crystal Structure of Thymidine Kinase with Dttp From U. Urealyticum

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

The structure of Crystal Structure of Thymidine Kinase with Dttp From U. Urealyticum, PDB code: 2uz3 was solved by M.Welin, U.Kosinska, N.E.Mikkelsen, C.Carnrot, C.Zhu, L.Wang, S.Eriksson, B.Munch-Petersen, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.01 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.789, 110.753, 73.034, 90.00, 109.86, 90.00
R / Rfree (%)	22 / 27.5

The structure of Crystal Structure of Thymidine Kinase with Dttp From U. Urealyticum also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Thymidine Kinase with Dttp From U. Urealyticum (pdb code 2uz3). 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 with Dttp From U. Urealyticum, PDB code: 2uz3:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 with Dttp From U. Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1218 b:55.3 occ:1.00 ND1 A:HIS194 2.2 52.7 1.0 SG A:CYS156 2.2 53.6 1.0 SG A:CYS153 2.2 47.7 1.0 SG A:CYS191 2.2 49.6 1.0 CE1 A:HIS194 3.0 52.4 1.0 CB A:CYS153 3.1 47.0 1.0 CG A:HIS194 3.3 52.6 1.0 CB A:CYS191 3.3 46.6 1.0 CB A:CYS156 3.6 52.3 1.0 N A:CYS191 3.7 45.5 1.0 CB A:HIS194 3.7 51.3 1.0 N A:CYS156 3.8 52.6 1.0 CA A:CYS191 4.1 46.4 1.0 NE2 A:HIS194 4.2 52.5 1.0 CB A:GLU155 4.2 53.9 1.0 CA A:CYS156 4.3 52.0 1.0 CD2 A:HIS194 4.3 52.7 1.0 CA A:CYS153 4.6 47.0 1.0 CB A:ALA158 4.7 47.5 1.0 N A:HIS194 4.7 51.5 1.0 C A:GLU155 4.8 53.1 1.0 C A:CYS191 4.8 46.8 1.0 N A:ALA158 4.9 48.3 1.0 C A:VAL190 4.9 44.9 1.0 CA A:HIS194 4.9 51.4 1.0 C A:CYS156 4.9 51.7 1.0 CA A:GLU155 4.9 53.2 1.0 N A:GLU155 5.0 52.3 1.0 N A:GLY157 5.0 50.9 1.0

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


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 with Dttp From U. Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2218 b:47.5 occ:1.00 ND1 B:HIS194 2.1 50.8 1.0 SG B:CYS156 2.3 50.2 1.0 SG B:CYS153 2.3 45.9 1.0 SG B:CYS191 2.3 46.5 1.0 CE1 B:HIS194 3.0 51.2 1.0 CG B:HIS194 3.2 51.7 1.0 CB B:CYS153 3.2 46.3 1.0 CB B:CYS191 3.4 46.0 1.0 CB B:CYS156 3.5 51.4 1.0 CB B:HIS194 3.6 51.1 1.0 N B:CYS156 3.7 52.5 1.0 N B:CYS191 3.9 45.3 1.0 NE2 B:HIS194 4.1 51.0 1.0 CA B:CYS156 4.2 51.7 1.0 CB B:GLU155 4.2 53.7 1.0 CD2 B:HIS194 4.2 50.9 1.0 CA B:CYS191 4.3 46.1 1.0 N B:HIS194 4.6 51.4 1.0 C B:GLU155 4.6 53.0 1.0 CA B:CYS153 4.7 46.8 1.0 CA B:HIS194 4.7 51.2 1.0 CA B:GLU155 4.7 53.1 1.0 N B:GLU155 4.8 52.4 1.0 CB B:ALA158 4.8 47.3 1.0 C B:CYS156 4.9 51.5 1.0 C B:CYS191 5.0 46.5 1.0 C B:VAL190 5.0 44.7 1.0 N B:GLY157 5.0 50.6 1.0

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


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 with Dttp From U. Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3218 b:47.0 occ:1.00 SG C:CYS191 2.0 42.5 1.0 ND1 C:HIS194 2.3 53.1 1.0 SG C:CYS153 2.3 46.4 1.0 SG C:CYS156 2.3 52.3 1.0 CE1 C:HIS194 3.1 52.2 1.0 CB C:CYS153 3.2 47.0 1.0 CG C:HIS194 3.4 52.1 1.0 CB C:CYS191 3.4 45.7 1.0 CB C:CYS156 3.5 51.7 1.0 CB C:HIS194 3.8 51.1 1.0 N C:CYS156 3.8 52.7 1.0 N C:CYS191 3.8 45.3 1.0 CA C:CYS191 4.2 46.0 1.0 CA C:CYS156 4.2 51.9 1.0 NE2 C:HIS194 4.3 52.2 1.0 CD2 C:HIS194 4.4 52.3 1.0 CB C:GLU155 4.6 53.5 1.0 CA C:CYS153 4.7 46.7 1.0 N C:HIS194 4.7 51.4 1.0 C C:GLU155 4.8 53.0 1.0 C C:CYS156 4.9 51.5 1.0 CB C:ALA158 4.9 47.9 1.0 N C:GLY157 4.9 50.8 1.0 N C:ALA158 4.9 48.3 1.0 CA C:HIS194 4.9 51.3 1.0 C C:CYS191 4.9 46.6 1.0 C C:VAL190 5.0 44.6 1.0 CA C:GLU155 5.0 53.2 1.0 N C:GLU155 5.0 52.3 1.0

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


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 with Dttp From U. Urealyticum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4218 b:50.8 occ:1.00 SG D:CYS156 2.2 53.3 1.0 SG D:CYS153 2.3 46.1 1.0 SG D:CYS191 2.3 45.5 1.0 ND1 D:HIS194 2.3 52.2 1.0 CB D:CYS153 3.2 46.7 1.0 CE1 D:HIS194 3.2 51.9 1.0 CB D:CYS191 3.3 45.8 1.0 CG D:HIS194 3.4 52.1 1.0 CB D:CYS156 3.5 51.8 1.0 CB D:HIS194 3.7 51.2 1.0 N D:CYS156 3.7 52.6 1.0 N D:CYS191 3.8 45.3 1.0 CA D:CYS191 4.2 46.1 1.0 CA D:CYS156 4.2 51.9 1.0 NE2 D:HIS194 4.4 51.7 1.0 CD2 D:HIS194 4.5 52.1 1.0 CB D:GLU155 4.6 53.5 1.0 CA D:CYS153 4.6 46.8 1.0 CB D:ALA158 4.7 47.4 1.0 N D:HIS194 4.7 51.5 1.0 C D:GLU155 4.7 53.0 1.0 CA D:HIS194 4.8 51.3 1.0 N D:GLU155 4.8 52.3 1.0 C D:CYS156 4.9 51.5 1.0 CA D:GLU155 4.9 53.1 1.0 C D:CYS191 4.9 46.6 1.0 C D:VAL190 4.9 44.7 1.0 N D:GLY157 4.9 50.7 1.0 N D:ALA158 4.9 48.3 1.0

M.Welin, U.Kosinska, N.E.Mikkelsen, C.Carnrot, C.Zhu, L.Wang, S.Eriksson, B.Munch-Petersen, H.Eklund. Structures of Thymidine Kinase 1 of Human and Mycoplasmic Origin Proc.Natl.Acad.Sci.Usa V. 101 17970 2004.
ISSN: ISSN 0027-8424
PubMed: 15611477
DOI: 10.1073/PNAS.0406332102