The binding sites of Sodium atom in the structure of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot (pdb code 1l2x). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1l2x structure was solved by M.EGLI, G.MINASOV, L.SU, A.RICH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 20.0-1.2 | | Space group | P3221 | | a (A) | 30.160 | | b (A) | 30.160 | | c (A) | 140.278 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 120.00 | | Rfactor (%) | 14.2 | | Rfree (%) | 20.7 |
|
Sodium binding site 1 out of 3 in 1l2x
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1l2x. 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: G6, A: G16, A: C17, A: A20, A: A21, A: C22, A: Hoh92, A: Hoh118, A: Hoh125, | conact list:
| Atom | Atom | Distance (A) | | Na | N3 A:G6 | 4.59 | | Na | N2 A:G6 | 4.39 | | Na | C2 A:G6 | 4.79 | | Na | N9 A:G16 | 4.12 | | Na | N3 A:G16 | 2.84 | | Na | N2 A:G16 | 3.57 | | Na | C3' A:G16 | 4.84 | | Na | C2 A:G16 | 3.63 | | Na | N1 A:G16 | 4.97 | | Na | C1' A:G16 | 3.52 | | Na | O4' A:G16 | 4.77 | | Na | C4 A:G16 | 3.85 | | Na | C2' A:G16 | 3.35 | | Na | O2' A:G16 | 2.88 | | Na | C1' A:C17 | 4.13 | | Na | O4' A:C17 | 3.81 | | Na | C4' A:C17 | 4.60 | | Na | O2' A:C17 | 4.59 | | Na | O3' A:A20 | 4.40 | | Na | N9 A:A21 | 4.58 | | Na | C8 A:A21 | 3.26 | | Na | C5 A:A21 | 4.42 | | Na | P A:A21 | 3.89 | | Na | N7 A:A21 | 3.09 | | Na | OP2 A:A21 | 2.69 | | Na | O5' A:A21 | 4.05 | | Na | C5 A:C22 | 4.58 | | Na | C4 A:C22 | 4.71 | | Na | N4 A:C22 | 4.02 | | Na | N4 A:C22 | 4.75 | | Na | O A:Hoh92 | 2.67 | | Na | O A:Hoh118 | 4.78 | | Na | O A:Hoh125 | 3.59 |
| interactive model:
| Sodium binding site 2 out of 3 in 1l2x
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1l2x. 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: C3, A: G4, A: G18, A: Hoh77, A: Hoh94, A: Hoh101, A: Hoh216, | conact list:
| Atom | Atom | Distance (A) | | Na | C3' A:C3 | 4.73 | | Na | C2 A:C3 | 3.84 | | Na | N1 A:C3 | 4.20 | | Na | C1' A:C3 | 3.49 | | Na | O2 A:C3 | 2.74 | | Na | O4' A:C3 | 4.68 | | Na | C2' A:C3 | 3.25 | | Na | O2' A:C3 | 2.71 | | Na | C1' A:G4 | 4.24 | | Na | O4' A:G4 | 3.37 | | Na | C5' A:G4 | 4.58 | | Na | C4' A:G4 | 4.23 | | Na | N2 A:G18 | 4.20 | | Na | O A:Hoh77 | 4.13 | | Na | O A:Hoh94 | 4.95 | | Na | O A:Hoh101 | 2.77 | | Na | O A:Hoh216 | 4.39 |
| interactive model:
| Sodium binding site 3 out of 3 in 1l2x
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1l2x. 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: C5, A: G6, A: A20, A: A21, A: Hoh108, A: Hoh165, | conact list:
| Atom | Atom | Distance (A) | | Na | C3' A:C5 | 4.69 | | Na | C1' A:C5 | 4.58 | | Na | O2 A:C5 | 4.74 | | Na | O3' A:C5 | 4.65 | | Na | C2' A:C5 | 3.58 | | Na | O2' A:C5 | 2.59 | | Na | C3' A:G6 | 4.76 | | Na | C1' A:G6 | 4.16 | | Na | O4' A:G6 | 3.05 | | Na | C5' A:G6 | 3.57 | | Na | C2' A:G6 | 4.92 | | Na | C4' A:G6 | 3.32 | | Na | O5' A:G6 | 4.57 | | Na | O2' A:G6 | 4.75 | | Na | N9 A:A20 | 4.40 | | Na | C3' A:A20 | 3.71 | | Na | C8 A:A20 | 3.81 | | Na | C1' A:A20 | 4.70 | | Na | N7 A:A20 | 4.38 | | Na | O3' A:A20 | 4.29 | | Na | C2' A:A20 | 3.91 | | Na | C4' A:A20 | 4.96 | | Na | OP1 A:A21 | 2.65 | | Na | P A:A21 | 3.96 | | Na | OP2 A:A21 | 4.87 | | Na | O A:Hoh108 | 3.78 | | Na | O A:Hoh165 | 3.85 |
| interactive model:
|
|