Sodium in the structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) At 1.4 A (BR1) (pdb 2r1s)

The binding sites of Sodium atom in the structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) At 1.4 A (BR1) (pdb code 2r1s). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2r1s structure was solved by Y.TIMSIT, S.BOMBARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 14.1-1.4 Space group P1 a (A) 25.380 b (A) 25.670 c (A) 29.920 alpha (°) 98.64 beta (°) 105.43 gamma (°) 100.67 Rfactor (%) 15.9 Rfree (%) 18.5 Sodium Binding Sites: Sodium binding site 1 out of 5 in 2r1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2r1s. 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: Hoh21, A: Hoh25, A: Hoh26, A: Hoh37, A: Hoh50, A: Hoh56, A: Hoh58, A: Hoh59, A: Hoh84, B: Hoh75, conact list: Atom Atom Distance (A) Na N3 A:U4 4.43 Na C6 A:U4 4.96 Na C5 A:U4 3.75 Na C4 A:U4 3.32 Na O4 A:U4 2.52 Na N3 A:U5 4.55 Na C5 A:U5 3.96 Na C4 A:U5 3.42 Na O4 A:U5 2.44 Na N6 B:A22 4.14 Na N6 B:A23 4.45 Na O A:Hoh20 4.53 Na O A:Hoh21 4.94 Na O A:Hoh25 4.28 Na O A:Hoh26 4.40 Na O A:Hoh37 2.31 Na O A:Hoh50 2.39 Na O A:Hoh56 2.51 Na O A:Hoh58 4.32 Na O A:Hoh59 2.44 Na O A:Hoh84 3.50 Na O B:Hoh75 4.64 interactive model: Sodium binding site 2 out of 5 in 2r1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2r1s. 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: 5bu6, A: G7, A: A8, A: Hoh31, A: Hoh52, A: Hoh61, A: Hoh72, A: Hoh75, A: Hoh76, A: Hoh100, conact list: Atom Atom Distance (A) Na C6 A:5bu6 4.86 Na C5 A:5bu6 4.51 Na C4 A:5bu6 4.76 Na BR A:5bu6 4.55 Na N9 A:G7 4.29 Na C8 A:G7 3.15 Na C6 A:G7 4.12 Na C5 A:G7 3.50 Na N7 A:G7 2.49 Na C4 A:G7 4.48 Na OP2 A:G7 4.27 Na O5' A:G7 4.84 Na O6 A:G7 4.05 Na OP2 A:A8 4.77 Na O A:Hoh31 2.50 Na O A:Hoh52 2.53 Na O A:Hoh61 2.74 Na O A:Hoh72 2.62 Na O A:Hoh75 3.92 Na O A:Hoh76 2.55 Na O A:Hoh100 4.70 interactive model: Sodium binding site 3 out of 5 in 2r1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2r1s. 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: Hoh53, A: Hoh61, A: Hoh71, A: Hoh75, A: Hoh81, A: Hoh85, A: Hoh88, A: Hoh100, A: Hoh102, B: Hoh65, B: Hoh96, conact list: Atom Atom Distance (A) Na C8 A:A8 4.88 Na C5 A:A8 4.92 Na N7 A:A8 4.52 Na N9 A:A9 4.64 Na C8 A:A9 3.44 Na C6 A:A9 4.12 Na C5 A:A9 3.60 Na N6 A:A9 3.81 Na N7 A:A9 2.57 Na C4 A:A9 4.72 Na OP2 A:A9 3.97 Na O A:Hoh53 2.48 Na O A:Hoh61 4.80 Na O A:Hoh71 2.59 Na O A:Hoh75 4.82 Na O A:Hoh81 3.89 Na O A:Hoh85 2.21 Na O A:Hoh88 2.59 Na O A:Hoh100 4.49 Na O A:Hoh102 2.42 Na O B:Hoh65 4.46 Na O B:Hoh96 4.76 interactive model: Sodium binding site 4 out of 5 in 2r1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 2r1s. 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: Na4, A: Hoh75, A: Hoh102, B: Hoh36, B: Hoh37, B: Hoh38, B: Hoh44, B: Hoh48, B: Hoh49, B: Hoh65, B: Hoh66, B: Hoh67, B: Hoh76, conact list: Atom Atom Distance (A) Na N6 A:A9 4.05 Na N6 A:A10 4.37 Na N3 B:U17 4.49 Na C5 B:U17 3.84 Na C4 B:U17 3.37 Na O4 B:U17 2.47 Na N3 B:U18 4.48 Na C5 B:U18 3.86 Na C4 B:U18 3.34 Na O4 B:U18 2.39 Na NA B:Na4 3.63 Na O A:Hoh75 4.72 Na O A:Hoh102 4.74 Na O B:Hoh36 4.39 Na O B:Hoh37 4.93 Na O B:Hoh38 4.52 Na O B:Hoh44 2.44 Na O B:Hoh48 4.24 Na O B:Hoh49 4.45 Na O B:Hoh65 2.40 Na O B:Hoh66 2.41 Na O B:Hoh67 2.52 Na O B:Hoh76 4.29 interactive model: Sodium binding site 5 out of 5 in 2r1s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 2r1s. 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: G16, B: U17, B: Na1, B: Hoh37, B: Hoh38, B: Hoh44, B: Hoh49, B: Hoh66, B: Hoh67, B: Hoh76, B: Hoh98, B: Hoh107, B: Hoh108, conact list: Atom Atom Distance (A) Na OP2 B:G16 4.15 Na C5 B:U17 4.88 Na OP2 B:U17 4.45 Na NA B:Na1 3.63 Na O B:Hoh37 4.03 Na O B:Hoh38 2.40 Na O B:Hoh44 4.19 Na O B:Hoh49 4.72 Na O B:Hoh66 2.34 Na O B:Hoh67 2.44 Na O B:Hoh76 4.54 Na O B:Hoh98 4.13 Na O B:Hoh107 2.42 Na O B:Hoh108 2.32 interactive model: