Magnesium in the structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase (pdb 2dya)

The binding sites of Magnesium atom in the structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase (pdb code 2dya). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2dya 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) 40.1-1.8 Space group P63 a (A) 69.707 b (A) 69.707 c (A) 107.117 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 11.4 Rfree (%) 16.9 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2dya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2dya. 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: Hoh718, A: Hoh719, A: Hoh720, A: Hoh721, A: Hoh724, A: Hoh725, A: Hoh747, A: Hoh749, A: Hoh803, conact list: Atom Atom Distance (A) Mg OE1 A:Glu57 4.57 Mg OE2 A:Glu57 4.14 Mg CD A:Glu57 4.57 Mg NE2 A:His58 4.33 Mg CE1 A:His58 4.98 Mg CZ A:Arg91 4.93 Mg NH2 A:Arg91 4.96 Mg NH1 A:Arg91 4.07 Mg ND1 A:His124 4.70 Mg CE1 A:His124 4.43 Mg O A:Ala125 4.90 Mg CB A:Asp127 4.93 Mg OD2 A:Asp127 4.56 Mg O3B A:Adp501 3.80 Mg PA A:Adp501 3.50 Mg O2A A:Adp501 4.53 Mg O1B A:Adp501 2.33 Mg PB A:Adp501 3.40 Mg C5' A:Adp501 4.40 Mg O5' A:Adp501 4.42 Mg O2B A:Adp501 4.82 Mg O3A A:Adp501 3.91 Mg O1A A:Adp501 2.12 Mg O A:Hoh718 2.58 Mg O A:Hoh719 4.62 Mg O A:Hoh720 2.35 Mg O A:Hoh721 2.53 Mg O A:Hoh724 4.34 Mg O A:Hoh725 4.33 Mg O A:Hoh747 4.79 Mg O A:Hoh749 3.48 Mg O A:Hoh803 4.97 interactive model: Magnesium binding site 2 out of 2 in 2dya Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2dya. 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: Glu57, B: His58, B: Arg91, B: His124, B: Asp127, B: Adp502, B: Hoh720, B: Hoh721, B: Hoh725, B: Hoh729, B: Hoh738, B: Hoh743, B: Hoh752, B: Hoh779, B: Hoh781, conact list: Atom Atom Distance (A) Mg OE2 B:Glu57 3.80 Mg CD B:Glu57 4.79 Mg NE2 B:His58 4.22 Mg CE1 B:His58 4.98 Mg NH1 B:Arg91 4.18 Mg ND1 B:His124 4.81 Mg CE1 B:His124 4.45 Mg CB B:Asp127 4.82 Mg OD2 B:Asp127 4.19 Mg CG B:Asp127 4.86 Mg O3B B:Adp502 4.07 Mg PA B:Adp502 3.59 Mg O2A B:Adp502 4.64 Mg O1B B:Adp502 2.24 Mg PB B:Adp502 3.46 Mg C5' B:Adp502 4.41 Mg O5' B:Adp502 4.46 Mg O2B B:Adp502 4.79 Mg O3A B:Adp502 3.99 Mg O1A B:Adp502 2.20 Mg O B:Hoh720 4.68 Mg O B:Hoh721 4.90 Mg O B:Hoh725 4.13 Mg O B:Hoh729 4.52 Mg O B:Hoh738 2.59 Mg O B:Hoh743 2.49 Mg O B:Hoh752 2.34 Mg O B:Hoh779 3.95 Mg O B:Hoh781 4.70 interactive model: