Sodium in the structure of Crystal Structure of The the Open Nak Channel-Low Na+ Complex (pdb 3e89)

The binding sites of Sodium atom in the structure of Crystal Structure of The the Open Nak Channel-Low Na+ Complex (pdb code 3e89). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3e89 structure was solved by Y.JIANG, A.ALAM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.8-1.8 Space group I4 a (A) 68.050 b (A) 68.050 c (A) 89.251 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 24.8 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3e89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3e89. 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: Thr63, A: Val64, A: Gly65, A: Cs1, A: Hoh508, conact list: Atom Atom Distance (A) Na O A:Thr63 4.61 Na O A:Val64 2.94 Na C A:Val64 4.01 Na N A:Gly65 4.57 Na C A:Gly65 4.72 Na CA A:Gly65 4.23 Na CS A:Cs1 2.45 Na O A:Hoh508 4.02 interactive model: Sodium binding site 2 out of 4 in 3e89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3e89. 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: Thr62, A: Thr63, A: Cs1, A: Hoh507, conact list: Atom Atom Distance (A) Na O A:Thr62 4.75 Na O A:Thr63 4.06 Na CB A:Thr63 3.35 Na CG2 A:Thr63 4.24 Na OG1 A:Thr63 2.43 Na C A:Thr63 4.46 Na CA A:Thr63 4.55 Na CS A:Cs1 4.94 Na O A:Hoh507 2.71 interactive model: Sodium binding site 3 out of 4 in 3e89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3e89. 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: Thr63, B: Val64, B: Gly65, B: Cs2, conact list: Atom Atom Distance (A) Na O B:Thr63 4.91 Na O B:Val64 3.16 Na C B:Val64 4.17 Na N B:Gly65 4.63 Na C B:Gly65 4.73 Na CA B:Gly65 4.17 Na CS B:Cs2 2.81 interactive model: Sodium binding site 4 out of 4 in 3e89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3e89. 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: Thr62, B: Thr63, B: Cs2, B: Hoh540, conact list: Atom Atom Distance (A) Na O B:Thr62 4.75 Na O B:Thr63 3.97 Na CB B:Thr63 3.42 Na CG2 B:Thr63 4.30 Na OG1 B:Thr63 2.47 Na C B:Thr63 4.46 Na CA B:Thr63 4.61 Na CS B:Cs2 4.79 Na O B:Hoh540 2.94 interactive model: