Magnesium in PDB 2qq0: Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp

All present enzymatic activity of Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp:
2.7.1.21;

The structure of Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp, PDB code: 2qq0 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)	28.00 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.160, 59.310, 61.300, 90.00, 103.02, 90.00
R / Rfree (%)	17.1 / 21.7

The structure of Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp (pdb code 2qq0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp, PDB code: 2qq0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg450 b:18.9 occ:1.00 O3G A:ANP601 2.0 28.6 1.0 O2B A:ANP601 2.0 14.7 1.0 O A:HOH749 2.1 20.7 1.0 OG1 A:THR17 2.1 14.7 1.0 O A:HOH617 2.2 19.5 1.0 O A:HOH616 2.2 16.6 1.0 PG A:ANP601 3.2 34.0 1.0 CB A:THR17 3.2 13.2 1.0 PB A:ANP601 3.3 16.1 1.0 N3B A:ANP601 3.5 22.3 1.0 O2A A:ANP601 3.9 19.6 1.0 N A:THR17 3.9 12.7 1.0 O1G A:ANP601 3.9 28.9 1.0 OD2 A:ASP83 4.0 23.0 1.0 OE2 A:GLU84 4.1 26.2 1.0 O A:HOH675 4.1 30.6 1.0 CA A:THR17 4.1 13.2 1.0 O A:HOH783 4.1 49.2 1.0 OD1 A:ASP83 4.2 19.0 1.0 CG2 A:THR17 4.3 15.3 1.0 O A:HOH643 4.3 26.3 1.0 O1B A:ANP601 4.3 16.3 1.0 O3A A:ANP601 4.3 19.1 1.0 O2G A:ANP601 4.4 33.3 1.0 CG A:ASP83 4.5 19.0 1.0 PA A:ANP601 4.6 18.0 1.0 O5' A:THM501 4.6 22.9 1.0 CD A:GLU84 4.6 26.8 1.0 O A:VAL51 4.7 41.3 1.0 CD2 A:HIS53 4.8 39.1 1.0 O A:HOH704 4.9 45.8 1.0 NE2 A:HIS53 4.9 40.7 1.0 NZ A:LYS16 4.9 11.6 1.0 CB A:LYS16 5.0 12.1 1.0

Magnesium binding site 2 out of 2 in the Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thymidine Kinase From Thermotoga Maritima in Complex with Thymidine + Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg452 b:17.1 occ:1.00 O2B B:ADP701 1.9 14.8 1.0 O1P B:TMP601 2.0 19.5 1.0 O B:HOH797 2.1 17.7 1.0 O B:HOH844 2.1 18.8 1.0 OG1 B:THR17 2.1 13.8 1.0 O B:HOH725 2.2 17.1 1.0 CB B:THR17 3.3 13.1 1.0 PB B:ADP701 3.3 14.9 1.0 P B:TMP601 3.4 23.3 1.0 O3B B:ADP701 3.6 19.0 1.0 O2A B:ADP701 3.9 20.2 1.0 OD2 B:ASP83 4.0 22.9 1.0 N B:THR17 4.0 12.5 1.0 O2P B:TMP601 4.0 26.1 1.0 O B:HOH717 4.0 22.9 1.0 OD1 B:ASP83 4.1 18.8 1.0 O3P B:TMP601 4.1 26.3 1.0 OE2 B:GLU84 4.1 26.1 1.0 CA B:THR17 4.2 13.3 1.0 O B:HOH798 4.2 26.3 1.0 O1B B:ADP701 4.3 15.3 1.0 CG2 B:THR17 4.3 16.1 1.0 O B:HOH848 4.4 49.2 1.0 O3A B:ADP701 4.4 16.4 1.0 CG B:ASP83 4.4 17.0 1.0 O5' B:TMP601 4.5 18.5 1.0 CD B:GLU84 4.6 25.6 1.0 CD2 B:HIS53 4.7 41.5 1.0 PA B:ADP701 4.7 18.4 1.0 NE2 B:HIS53 4.7 42.1 1.0 CB B:LYS16 4.9 12.8 1.0 NZ B:LYS16 4.9 11.1 1.0 OE1 B:GLU84 5.0 25.1 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