Sodium in the structure of X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 At Ultra-High Resolution (pdb 1j8g)

The binding sites of Sodium atom in the structure of X-Ray Analysis of A Rna Tetraplex R(Uggggu)4 At Ultra-High Resolution (pdb code 1j8g). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1j8g structure was solved by J.DENG, Y.XIONG, M.SUNDARALINGAM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-0.6 Space group P4212 a (A) 36.154 b (A) 36.154 c (A) 74.134 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) 11.2 Sodium Binding Sites: Sodium binding site 1 out of 3 in 1j8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1j8g. 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: G5, A: U6, A: Sr505, A: Na512, conact list: Atom Atom Distance (A) Na C6 A:G5 4.58 Na N1 A:G5 4.84 Na O6 A:G5 4.14 Na N3 A:U6 3.47 Na C2 A:U6 4.72 Na C5 A:U6 4.50 Na C4 A:U6 3.20 Na O4 A:U6 2.35 Na SR A:Sr505 4.87 Na NA A:Na512 0.00 Na NA A:Na512 1.64 interactive model: Sodium binding site 2 out of 3 in 1j8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1j8g. 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: G5, A: U6, A: Sr505, A: Na512, conact list: Atom Atom Distance (A) Na C6 A:G5 3.61 Na N1 A:G5 3.96 Na C5 A:G5 4.71 Na O6 A:G5 2.89 Na N3 A:U6 3.83 Na C5 A:U6 4.94 Na C4 A:U6 3.58 Na O4 A:U6 2.61 Na SR A:Sr505 3.23 Na NA A:Na512 1.64 Na NA A:Na512 0.00 interactive model: Sodium binding site 3 out of 3 in 1j8g Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1j8g. 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: G15, B: U16, B: Sr507, B: Hoh101, B: Hoh170, conact list: Atom Atom Distance (A) Na C6 B:G15 4.13 Na N1 B:G15 4.43 Na O6 B:G15 3.59 Na N3 B:U16 3.59 Na C2 B:U16 4.87 Na C5 B:U16 4.65 Na C4 B:U16 3.31 Na O4 B:U16 2.37 Na SR B:Sr507 4.24 Na O B:Hoh101 2.40 Na O B:Hoh170 4.42 interactive model: