Magnesium in the structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex With Adp (pdb 2dy9)

The binding sites of Magnesium atom in the structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex With Adp (pdb code 2dy9). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2dy9 structure was solved by M.KATO-MURAYAMA, K.MURAYAMA, T.TERADA, M.SHIROUZU, S.YOKOYAMA, RIKENSTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.9-2.0 Space group P63 a (A) 69.835 b (A) 69.835 c (A) 106.897 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 12.2 Rfree (%) 16.8 Magnesium Binding Sites: Magnesium binding site 1 out of 1 in 2dy9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2dy9. 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: Glu57, A: His58, A: Arg91, A: His124, A: Ala125, A: Asp127, A: Adp501, A: Hoh714, A: Hoh730, A: Hoh732, A: Hoh735, A: Hoh736, A: Hoh764, A: Hoh766, A: Hoh774, A: Hoh794, conact list: Atom Atom Distance (A) Mg OE1 A:Glu57 4.50 Mg OE2 A:Glu57 4.14 Mg CD A:Glu57 4.56 Mg NE2 A:His58 4.53 Mg CZ A:Arg91 4.82 Mg NH2 A:Arg91 4.73 Mg NH1 A:Arg91 4.07 Mg ND1 A:His124 4.79 Mg CE1 A:His124 4.41 Mg O A:Ala125 4.82 Mg CB A:Asp127 4.77 Mg OD2 A:Asp127 4.31 Mg CG A:Asp127 4.80 Mg O3B A:Adp501 4.14 Mg PA A:Adp501 3.71 Mg O2A A:Adp501 4.68 Mg O1B A:Adp501 2.48 Mg PB A:Adp501 3.65 Mg C5' A:Adp501 4.58 Mg O5' A:Adp501 4.64 Mg O3A A:Adp501 4.17 Mg O1A A:Adp501 2.29 Mg O A:Hoh714 4.86 Mg O A:Hoh730 4.47 Mg O A:Hoh732 2.61 Mg O A:Hoh735 2.26 Mg O A:Hoh736 4.18 Mg O A:Hoh764 3.63 Mg O A:Hoh766 4.52 Mg O A:Hoh774 2.39 Mg O A:Hoh794 4.86 interactive model: