Sodium in the structure of Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 (pdb 3gnk)

The binding sites of Sodium atom in the structure of Calcium Bound to the Holliday Junction Sequence D(Tcggcgccga)4 (pdb code 3gnk). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3gnk structure was solved by A.NASEER, C.J.CARDIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 16.4-2.1 Space group C121 a (A) 65.970 b (A) 24.170 c (A) 73.890 alpha (°) 90.00 beta (°) 110.37 gamma (°) 90.00 Rfactor (%) 21.4 Rfree (%) 30.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3gnk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3gnk. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dg9, B: Dc12, B: Dg13, B: Dg14, A: Hoh100, A: Hoh182, B: Hoh101, B: Hoh103, B: Hoh105, B: Hoh107, B: Hoh108, B: Hoh109, B: Hoh181, B: Hoh183, conact list: Atom Atom Distance (A) Na N2 A:Dg9 4.11 Na O2 B:Dc12 4.66 Na N3 B:Dg13 4.22 Na N2 B:Dg13 4.63 Na C2 B:Dg13 4.80 Na C1' B:Dg13 4.76 Na O4' B:Dg13 3.89 Na C4' B:Dg13 4.46 Na O4' B:Dg14 4.52 Na C5' B:Dg14 4.98 Na O A:Hoh100 4.59 Na O A:Hoh182 2.09 Na O B:Hoh101 4.37 Na O B:Hoh103 4.76 Na O B:Hoh105 2.39 Na O B:Hoh107 2.57 Na O B:Hoh108 2.18 Na O B:Hoh109 4.90 Na O B:Hoh181 2.31 Na O B:Hoh183 4.49 interactive model: Sodium binding site 2 out of 2 in 3gnk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3gnk. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Dt1, A: Dc2, A: Dg3, D: Dc35, D: Dg36, D: Dc37, D: Dc38, A: Hoh44, A: Hoh55, A: Hoh126, C: Hoh144, C: Hoh176, D: Hoh41, D: Hoh125, D: Hoh130, D: Hoh165, D: Hoh177, conact list: Atom Atom Distance (A) Na O5' A:Dt1 4.52 Na C6 A:Dc2 4.47 Na C5 A:Dc2 3.97 Na O6 A:Dg3 4.93 Na O3' D:Dc35 4.65 Na OP1 D:Dg36 4.76 Na C5' D:Dg36 3.62 Na C4' D:Dg36 4.32 Na O5' D:Dg36 4.80 Na OP2 D:Dc37 4.47 Na N4 D:Dc38 4.62 Na O A:Hoh44 4.31 Na O A:Hoh55 4.96 Na O A:Hoh126 2.41 Na O C:Hoh144 3.85 Na O C:Hoh176 4.10 Na O D:Hoh41 2.97 Na O D:Hoh125 2.72 Na O D:Hoh130 4.58 Na O D:Hoh165 2.52 Na O D:Hoh177 4.84 interactive model: