Magnesium in the structure of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Tdp (pdb 2v54)

The binding sites of Magnesium atom in the structure of Crystal Structure of Vaccinia Virus Thymidylate Kinase Bound to Tdp (pdb code 2v54). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2v54 structure was solved by C.CAILLAT, D.TOPALIS, L.A.AGROFOGLIO, S.POCHET, J.BALZARINI, D.DEVILLE-BONNE, P.MEYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.4 Space group P212121 a (A) 56.770 b (A) 55.590 c (A) 161.170 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.63 Rfree (%) 27.6 Magnesium Binding Sites: Magnesium binding site 1 out of 1 in 2v54 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2v54. 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: B: Asp13, B: Lys14, B: Glu142, B: Glu145, B: Pop1206, B: Tyd1207, B: Hoh2046, conact list: Atom Atom Distance (A) Mg CB B:Asp13 3.90 Mg OD2 B:Asp13 4.47 Mg OD1 B:Asp13 2.28 Mg CG B:Asp13 3.40 Mg CA B:Asp13 4.59 Mg N B:Lys14 4.99 Mg CE B:Lys14 4.73 Mg NZ B:Lys14 4.53 Mg CB B:Glu142 4.88 Mg OE2 B:Glu142 3.77 Mg CD B:Glu142 4.64 Mg OE1 B:Glu145 4.73 Mg OE2 B:Glu145 2.54 Mg CD B:Glu145 3.71 Mg CG B:Glu145 4.28 Mg O B:Pop1206 4.54 Mg O5 B:Pop1206 3.29 Mg P2 B:Pop1206 3.34 Mg O3 B:Pop1206 4.50 Mg O4 B:Pop1206 2.26 Mg O6 B:Pop1206 4.18 Mg O3B B:Tyd1207 3.55 Mg C3' B:Tyd1207 4.45 Mg C3' B:Tyd1207 4.46 Mg O1B B:Tyd1207 4.50 Mg PB B:Tyd1207 3.31 Mg O3' B:Tyd1207 4.54 Mg O3' B:Tyd1207 4.46 Mg C5' B:Tyd1207 4.41 Mg C5' B:Tyd1207 4.42 Mg C4' B:Tyd1207 4.82 Mg C4' B:Tyd1207 4.84 Mg O5' B:Tyd1207 4.86 Mg O5' B:Tyd1207 4.93 Mg O2B B:Tyd1207 2.04 Mg O3A B:Tyd1207 4.07 Mg O1A B:Tyd1207 3.92 Mg O B:Hoh2046 1.84 interactive model: