Magnesium in the structure of Human Thymidylate Kinase Complexed With Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion (pdb 1e2d)

The binding sites of Magnesium atom in the structure of Human Thymidylate Kinase Complexed With Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion (pdb code 1e2d). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1e2d structure 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, brief refinement statistics is given in the table below: Resolution (A) 33.4-1.6 Space group P43212 a (A) 101.000 b (A) 101.000 c (A) 49.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 24.2 Magnesium Binding Sites: Magnesium binding site 1 out of 3 in 1e2d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1e2d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys19, A: Ser20, A: Asp96, A: Tmp301, A: Adp302, A: Hoh2016, A: Hoh2017, A: Hoh2037, A: Hoh2141, A: Hoh2147, A: Hoh2274, A: Hoh2280, A: Hoh2287, A: Hoh2290, conact list: Atom Atom Distance (A) Mg CB A:Lys19 4.73 Mg CE A:Lys19 4.74 Mg C A:Lys19 4.98 Mg N A:Ser20 3.92 Mg CB A:Ser20 3.22 Mg OG A:Ser20 2.13 Mg CA A:Ser20 4.15 Mg OD2 A:Asp96 4.09 Mg OD1 A:Asp96 4.32 Mg CG A:Asp96 4.66 Mg P A:Tmp301 4.25 Mg O3P A:Tmp301 4.28 Mg O1P A:Tmp301 4.24 Mg O2P A:Tmp301 3.95 Mg O3B A:Adp302 3.57 Mg PA A:Adp302 4.65 Mg O2A A:Adp302 4.96 Mg O1B A:Adp302 4.38 Mg PB A:Adp302 3.32 Mg O2B A:Adp302 2.03 Mg O3A A:Adp302 4.32 Mg O1A A:Adp302 4.11 Mg O A:Hoh2016 4.26 Mg O A:Hoh2017 4.69 Mg O A:Hoh2037 2.11 Mg O A:Hoh2141 4.22 Mg O A:Hoh2147 4.27 Mg O A:Hoh2274 2.12 Mg O A:Hoh2280 2.12 Mg O A:Hoh2287 4.94 Mg O A:Hoh2290 2.06 interactive model: Magnesium binding site 2 out of 3 in 1e2d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1e2d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Asp115, A: Gln119, A: Hoh2076, A: Hoh2159, A: Hoh2164, A: Hoh2166, conact list: Atom Atom Distance (A) Mg OD2 A:Asp115 4.37 Mg OD1 A:Asp115 4.38 Mg CG A:Asp115 4.83 Mg NE2 A:Gln119 4.71 Mg OE1 A:Gln119 4.11 Mg CD A:Gln119 4.41 Mg O A:Hoh2076 2.06 Mg O A:Hoh2159 2.09 Mg O A:Hoh2164 3.84 Mg O A:Hoh2166 1.96 interactive model: Magnesium binding site 3 out of 3 in 1e2d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1e2d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu149, A: Tmp301, A: Hoh2014, A: Hoh2015, A: Hoh2017, A: Hoh2026, A: Hoh2031, A: Hoh2079, A: Hoh2147, A: Hoh2192, A: Hoh2194, A: Hoh2272, A: Hoh2273, A: Hoh2274, A: Hoh2275, A: Hoh2287, conact list: Atom Atom Distance (A) Mg OE1 A:Glu149 4.75 Mg OE2 A:Glu149 4.20 Mg CD A:Glu149 4.44 Mg P A:Tmp301 4.71 Mg O3P A:Tmp301 4.03 Mg O1P A:Tmp301 4.04 Mg O A:Hoh2014 2.18 Mg O A:Hoh2015 2.26 Mg O A:Hoh2017 4.08 Mg O A:Hoh2026 3.87 Mg O A:Hoh2031 3.59 Mg O A:Hoh2079 4.21 Mg O A:Hoh2147 2.36 Mg O A:Hoh2192 3.79 Mg O A:Hoh2194 2.12 Mg O A:Hoh2272 2.29 Mg O A:Hoh2273 2.18 Mg O A:Hoh2274 4.35 Mg O A:Hoh2275 4.67 Mg O A:Hoh2287 4.97 interactive model: