Sodium in the structure of Gga Duplex A-Dna (pdb 1zfa)

The binding sites of Sodium atom in the structure of Gga Duplex A-Dna (pdb code 1zfa). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1zfa structure was solved by F.A.HAYS, A.T.TEEGARDEN, Z.J.R.JONES, M.HARMS, D.RAUP, J.WATSON, E.CAVALIERE, P.S.HO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.2-1.6 Space group P212121 a (A) 23.930 b (A) 44.620 c (A) 46.780 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.1 Rfree (%) 30 Sodium Binding Sites: Sodium binding site 1 out of 3 in 1zfa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1zfa. 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, A: Dg10, A: Hoh34, A: Hoh37, A: Hoh83, A: Hoh116, A: Hoh132, conact list: Atom Atom Distance (A) Na C8 A:Dg9 4.69 Na C5 A:Dg9 4.91 Na N7 A:Dg9 4.32 Na OP2 A:Dg9 4.54 Na N7 A:Dg10 4.72 Na OP2 A:Dg10 4.28 Na O A:Hoh34 2.24 Na O A:Hoh37 4.15 Na O A:Hoh83 2.09 Na O A:Hoh116 3.02 Na O A:Hoh132 4.42 interactive model: Sodium binding site 2 out of 3 in 1zfa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1zfa. 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: Dg20, B: Hoh68, B: Hoh73, B: Hoh141, conact list: Atom Atom Distance (A) Na OP1 B:Dg20 4.37 Na O B:Hoh68 2.99 Na O B:Hoh73 2.29 Na O B:Hoh141 2.87 interactive model: Sodium binding site 3 out of 3 in 1zfa Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1zfa. 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: Dg19, B: Dg20, B: Hoh36, B: Hoh78, B: Hoh82, B: Hoh86, B: Hoh96, B: Hoh129, B: Hoh142, B: Hoh144, B: Hoh156, conact list: Atom Atom Distance (A) Na N7 B:Dg19 4.33 Na O6 B:Dg19 4.64 Na N7 B:Dg20 4.51 Na O6 B:Dg20 4.70 Na O B:Hoh36 2.43 Na O B:Hoh78 3.53 Na O B:Hoh82 2.72 Na O B:Hoh86 4.71 Na O B:Hoh96 4.87 Na O B:Hoh129 4.80 Na O B:Hoh142 2.32 Na O B:Hoh144 3.09 Na O B:Hoh156 3.28 interactive model: