Sodium in the structure of Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) At 1.5 A (Natmn) (pdb 2r22)

The binding sites of Sodium atom in the structure of Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) At 1.5 A (Natmn) (pdb code 2r22). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2r22 structure was solved by Y.TIMSIT, S.BOMBARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.4 Space group P1 a (A) 25.280 b (A) 25.500 c (A) 29.600 alpha (°) 97.97 beta (°) 106.69 gamma (°) 101.62 Rfactor (%) 17.8 Rfree (%) 20 Sodium Binding Sites: Sodium binding site 1 out of 4 in 2r22 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2r22. 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: U4, A: U5, B: A22, B: A23, A: Hoh20, A: Hoh25, A: Hoh26, A: Hoh37, A: Hoh48, A: Hoh51, A: Hoh53, B: Hoh69, B: Hoh70, conact list: Atom Atom Distance (A) Na N3 A:U4 4.51 Na C6 A:U4 4.91 Na C5 A:U4 3.70 Na C4 A:U4 3.37 Na O4 A:U4 2.63 Na N3 A:U5 4.82 Na C5 A:U5 4.27 Na C4 A:U5 3.72 Na O4 A:U5 2.73 Na N6 B:A22 4.23 Na N6 B:A23 4.80 Na O A:Hoh20 4.48 Na O A:Hoh25 4.62 Na O A:Hoh26 4.24 Na O A:Hoh37 2.21 Na O A:Hoh48 2.39 Na O A:Hoh51 2.38 Na O A:Hoh53 4.22 Na O B:Hoh69 2.94 Na O B:Hoh70 4.45 interactive model: Sodium binding site 2 out of 4 in 2r22 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2r22. 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: U6, A: G7, A: A8, A: Hoh31, A: Hoh55, A: Hoh65, A: Hoh67, A: Hoh83, A: Hoh84, conact list: Atom Atom Distance (A) Na C6 A:U6 4.92 Na C5 A:U6 4.61 Na C4 A:U6 4.87 Na OP2 A:U6 4.96 Na N9 A:G7 4.37 Na C8 A:G7 3.22 Na C6 A:G7 4.12 Na C5 A:G7 3.53 Na N7 A:G7 2.51 Na C4 A:G7 4.54 Na OP2 A:G7 4.19 Na O5' A:G7 4.83 Na O6 A:G7 4.01 Na N7 A:A8 4.99 Na OP2 A:A8 4.64 Na O A:Hoh31 2.41 Na O A:Hoh55 2.57 Na O A:Hoh65 2.46 Na O A:Hoh67 2.55 Na O A:Hoh83 2.38 Na O A:Hoh84 4.15 interactive model: Sodium binding site 3 out of 4 in 2r22 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2r22. 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: A8, A: A9, A: Hoh50, A: Hoh55, A: Hoh64, A: Hoh71, A: Hoh73, A: Hoh75, conact list: Atom Atom Distance (A) Na N7 A:A8 4.73 Na N9 A:A9 4.82 Na C8 A:A9 3.65 Na C6 A:A9 4.15 Na C5 A:A9 3.71 Na N6 A:A9 3.78 Na N7 A:A9 2.75 Na C4 A:A9 4.85 Na OP2 A:A9 4.11 Na O A:Hoh50 2.39 Na O A:Hoh55 4.88 Na O A:Hoh64 2.71 Na O A:Hoh71 3.94 Na O A:Hoh73 2.27 Na O A:Hoh75 2.47 interactive model: Sodium binding site 4 out of 4 in 2r22 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2r22. 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: A9, A: A10, B: U17, B: U18, B: Hoh35, B: Hoh36, B: Hoh37, B: Hoh42, B: Hoh46, B: Hoh47, B: Hoh61, B: Hoh62, B: Hoh71, conact list: Atom Atom Distance (A) Na N6 A:A9 3.87 Na N6 A:A10 4.46 Na N3 B:U17 4.51 Na C5 B:U17 3.79 Na C4 B:U17 3.37 Na O4 B:U17 2.52 Na N3 B:U18 4.40 Na C5 B:U18 3.92 Na C4 B:U18 3.33 Na O4 B:U18 2.38 Na O B:Hoh35 4.25 Na O B:Hoh36 4.98 Na O B:Hoh37 4.24 Na O B:Hoh42 2.51 Na O B:Hoh46 4.15 Na O B:Hoh47 4.13 Na O B:Hoh61 2.38 Na O B:Hoh62 2.46 Na O B:Hoh71 4.41 interactive model: