Sodium in the structure of Crystal Structure of Intercalated Four-Stranded D(C3T) (pdb 191d)

The binding sites of Sodium atom in the structure of Crystal Structure of Intercalated Four-Stranded D(C3T) (pdb code 191d). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 191d structure was solved by C.KANG, I.BERGER, C.LOCKSHIN, R.RATLIFF, R.MOYZIS, A.RICH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.4 Space group C2221 a (A) 28.281 b (A) 44.341 c (A) 50.472 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 22.5 Sodium Binding Sites: Sodium binding site 1 out of 3 in 191d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 191d. 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: Dc1, A: Dc2, A: Hoh44, A: Hoh64, conact list: Atom Atom Distance (A) Na C3' A:Dc1 3.57 Na C6 A:Dc1 4.84 Na O3' A:Dc1 3.68 Na C5' A:Dc1 3.71 Na C2' A:Dc1 4.82 Na C4' A:Dc1 4.34 Na OP1 A:Dc2 4.13 Na P A:Dc2 3.57 Na OP2 A:Dc2 2.68 Na O5' A:Dc2 4.97 Na O A:Hoh44 3.45 Na O A:Hoh64 4.47 interactive model: Sodium binding site 2 out of 3 in 191d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 191d. 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: B: Dc7, B: Dt8, D: Dc13, D: Hoh46, D: Hoh69, conact list: Atom Atom Distance (A) Na C3' B:Dc7 3.94 Na C6 B:Dc7 4.50 Na O3' B:Dc7 4.37 Na C2' B:Dc7 4.03 Na OP1 B:Dt8 2.86 Na C3' B:Dt8 4.22 Na C6 B:Dt8 4.40 Na N1 B:Dt8 4.75 Na C1' B:Dt8 4.74 Na P B:Dt8 3.70 Na OP2 B:Dt8 5.00 Na C5' B:Dt8 4.66 Na C2' B:Dt8 3.62 Na C4' B:Dt8 4.91 Na O5' B:Dt8 3.41 Na H41 D:Dc13 4.00 Na N4 D:Dc13 4.91 Na O D:Hoh46 4.57 Na O D:Hoh69 2.84 interactive model: Sodium binding site 3 out of 3 in 191d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 191d. 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: C: Dc10, C: Dc11, C: Dt12, A: Hoh75, C: Hoh23, C: Hoh35, C: Hoh42, conact list: Atom Atom Distance (A) Na OP1 C:Dc10 4.31 Na P C:Dc10 4.48 Na OP2 C:Dc10 3.95 Na O5' C:Dc10 4.75 Na OP2 C:Dc11 3.59 Na HO3' C:Dt12 4.15 Na O3' C:Dt12 4.29 Na O A:Hoh75 4.31 Na O C:Hoh23 3.54 Na O C:Hoh35 3.09 Na O C:Hoh42 3.10 interactive model: