Calcium in the structure of Calcium Form of D(Cgcgaattcgcg)2 (pdb 463d)

The binding sites of Calcium atom in the structure of Calcium Form of D(Cgcgaattcgcg)2 (pdb code 463d). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 463d structure was solved by J.LIU, J.A.SUBIRANA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-1.4 Space group H3 a (A) 41.117 b (A) 41.117 c (A) 99.912 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 21.7 Rfree (%) 25.7 Calcium Binding Sites: Calcium binding site 1 out of 4 in 463d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 463d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg4, A: Da5, A: Da6, B: Dc21, B: Dg22, A: Hoh112, A: Hoh113, A: Hoh115, A: Hoh116, A: Hoh117, A: Hoh176, A: Hoh216, B: Hoh111, B: Hoh114, B: Hoh177, conact list: Atom Atom Distance (A) Ca N2 A:Dg4 4.37 Ca O4' A:Da5 4.92 Ca O4' A:Da6 4.63 Ca C5' A:Da6 4.66 Ca C4' A:Da6 4.75 Ca O2 B:Dc21 4.49 Ca O4' B:Dg22 4.56 Ca C5' B:Dg22 4.89 Ca C4' B:Dg22 4.78 Ca O A:Hoh112 2.60 Ca O A:Hoh113 2.42 Ca O A:Hoh115 2.43 Ca O A:Hoh116 2.44 Ca O A:Hoh117 2.34 Ca O A:Hoh176 4.66 Ca O A:Hoh216 4.63 Ca O B:Hoh111 2.50 Ca O B:Hoh114 2.32 Ca O B:Hoh177 4.39 interactive model: Calcium binding site 2 out of 4 in 463d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 463d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg4, A: Da5, A: Hoh125, A: Hoh188, A: Hoh244, conact list: Atom Atom Distance (A) Ca O3' A:Dg4 4.71 Ca OP1 A:Da5 2.24 Ca P A:Da5 3.49 Ca OP2 A:Da5 3.99 Ca C5' A:Da5 4.41 Ca O5' A:Da5 4.15 Ca O A:Hoh125 2.37 Ca O A:Hoh188 4.79 Ca O A:Hoh244 4.26 interactive model: Calcium binding site 3 out of 4 in 463d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 463d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dc9, A: Dg10, B: Dg16, B: Da17, B: Da18, A: Hoh119, A: Hoh122, A: Hoh154, A: Hoh225, B: Hoh118, B: Hoh120, B: Hoh121, B: Hoh123, B: Hoh124, B: Hoh153, conact list: Atom Atom Distance (A) Ca O2 A:Dc9 4.64 Ca O4' A:Dg10 4.60 Ca C4' A:Dg10 4.97 Ca N2 B:Dg16 4.47 Ca N3 B:Da17 4.85 Ca C1' B:Da17 4.83 Ca O3' B:Da17 4.68 Ca O4' B:Da17 4.38 Ca C4' B:Da17 4.94 Ca O4' B:Da18 4.46 Ca C5' B:Da18 4.12 Ca C4' B:Da18 4.47 Ca O5' B:Da18 4.92 Ca O A:Hoh119 2.27 Ca O A:Hoh122 2.12 Ca O A:Hoh154 4.42 Ca O A:Hoh225 4.56 Ca O B:Hoh118 2.13 Ca O B:Hoh120 2.22 Ca O B:Hoh121 2.23 Ca O B:Hoh123 2.27 Ca O B:Hoh124 2.15 Ca O B:Hoh153 4.43 interactive model: Calcium binding site 4 out of 4 in 463d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 463d. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Dc23, B: Dg24, B: Hoh126, B: Hoh155, B: Hoh187, conact list: Atom Atom Distance (A) Ca O3' B:Dc23 4.06 Ca OP1 B:Dg24 2.17 Ca P B:Dg24 3.48 Ca OP2 B:Dg24 4.28 Ca C5' B:Dg24 4.85 Ca O5' B:Dg24 4.69 Ca O B:Hoh126 2.20 Ca O B:Hoh155 4.99 Ca O B:Hoh187 4.47 interactive model: