Magnesium in PDB 1e2d: Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion

All present enzymatic activity of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion:
2.7.4.9;

The structure of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion, PDB code: 1e2d was solved by N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.40 / 1.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.000, 101.000, 49.800, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.2

The binding sites of Magnesium atom in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion (pdb code 1e2d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion, PDB code: 1e2d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:13.4 occ:1.00 O2B A:ADP302 2.0 11.5 1.0 O A:HOH2290 2.1 15.1 1.0 O A:HOH2037 2.1 15.4 1.0 O A:HOH2274 2.1 14.3 1.0 O A:HOH2280 2.1 13.2 1.0 OG A:SER20 2.1 12.7 1.0 CB A:SER20 3.2 11.8 1.0 PB A:ADP302 3.3 13.2 1.0 O3B A:ADP302 3.6 15.7 1.0 N A:SER20 3.9 13.2 1.0 O2P A:TMP301 4.0 18.2 1.0 OD2 A:ASP96 4.1 14.4 1.0 O1A A:ADP302 4.1 15.9 1.0 CA A:SER20 4.2 11.9 1.0 O A:HOH2141 4.2 16.3 1.0 O1P A:TMP301 4.2 24.4 1.0 P A:TMP301 4.3 22.4 1.0 O A:HOH2016 4.3 27.2 1.0 O A:HOH2147 4.3 26.8 1.0 O3P A:TMP301 4.3 25.1 1.0 OD1 A:ASP96 4.3 13.9 1.0 O3A A:ADP302 4.3 15.5 1.0 O1B A:ADP302 4.4 14.3 1.0 PA A:ADP302 4.7 14.8 1.0 CG A:ASP96 4.7 13.6 1.0 O A:HOH2017 4.7 32.6 1.0 CB A:LYS19 4.7 10.8 1.0 CE A:LYS19 4.7 17.0 1.0 O A:HOH2287 4.9 26.0 1.0 O2A A:ADP302 5.0 17.0 1.0 C A:LYS19 5.0 11.6 1.0

Magnesium binding site 2 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.4 occ:0.50 O A:HOH2166 2.0 22.7 1.0 O A:HOH2076 2.1 32.2 1.0 O A:HOH2159 2.1 22.8 1.0 O A:HOH2164 3.8 44.9 1.0 OE1 A:GLN119 4.1 15.9 1.0 OD2 A:ASP115 4.4 23.8 1.0 OD1 A:ASP115 4.4 24.1 1.0 CD A:GLN119 4.4 15.8 1.0 NE2 A:GLN119 4.7 15.4 1.0 CG A:ASP115 4.8 22.9 1.0

Magnesium binding site 3 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:32.0 occ:1.00 O A:HOH2194 2.1 26.9 1.0 O A:HOH2014 2.2 36.2 1.0 O A:HOH2273 2.2 25.3 1.0 O A:HOH2015 2.3 35.7 1.0 O A:HOH2272 2.3 36.4 1.0 O A:HOH2147 2.4 26.8 1.0 O A:HOH2031 3.6 43.9 1.0 O A:HOH2192 3.8 32.2 1.0 O A:HOH2026 3.9 53.3 1.0 O3P A:TMP301 4.0 25.1 1.0 O1P A:TMP301 4.0 24.4 1.0 O A:HOH2017 4.1 32.6 1.0 OE2 A:GLU149 4.2 31.6 1.0 O A:HOH2079 4.2 21.7 1.0 O A:HOH2274 4.4 14.3 1.0 CD A:GLU149 4.4 37.1 1.0 O A:HOH2275 4.7 27.1 1.0 P A:TMP301 4.7 22.4 1.0 OE1 A:GLU149 4.7 33.5 1.0 O A:HOH2287 5.0 26.0 1.0

N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, A.Lavie. Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained From Crystal Structures of Enzyme Complexes Along the Reaction Coordinate Structure V. 8 629 2000.
ISSN: ISSN 0969-2126
PubMed: 10873853
DOI: 10.1016/S0969-2126(00)00149-0