Sodium in the structure of High Resolution Crystal Structure of the Open Nak Channel Pore (pdb 3e86)

The binding sites of Sodium atom in the structure of High Resolution Crystal Structure of the Open Nak Channel Pore (pdb code 3e86). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3e86 structure was solved by Y.JIANG, A.ALAM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.0-1.6 Space group I4 a (A) 68.030 b (A) 68.030 c (A) 89.264 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.2 Rfree (%) 24.2 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3e86. 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: Hoh510, conact list: Atom Atom Distance (A) Na O A:Thr63 4.51 Na O A:Val64 2.94 Na C A:Val64 4.00 Na N A:Gly65 4.56 Na C A:Gly65 4.81 Na CA A:Gly65 4.25 Na CS A:Cs1 2.43 Na O A:Hoh510 4.00 interactive model: Sodium binding site 2 out of 4 in 3e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3e86. 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: Hoh506, A: Hoh545, A: Hoh548, conact list: Atom Atom Distance (A) Na O A:Thr62 4.78 Na O A:Thr63 4.11 Na CB A:Thr63 3.30 Na CG2 A:Thr63 4.17 Na OG1 A:Thr63 2.35 Na C A:Thr63 4.51 Na CA A:Thr63 4.55 Na CS A:Cs1 4.95 Na O A:Hoh506 4.09 Na O A:Hoh545 2.67 Na O A:Hoh548 4.66 interactive model: Sodium binding site 3 out of 4 in 3e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3e86. 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: Hoh566, conact list: Atom Atom Distance (A) Na O B:Thr62 4.74 Na O B:Thr63 4.01 Na CB B:Thr63 3.44 Na CG2 B:Thr63 4.31 Na OG1 B:Thr63 2.42 Na C B:Thr63 4.48 Na CA B:Thr63 4.62 Na CS B:Cs2 4.86 Na O B:Hoh566 2.71 interactive model: Sodium binding site 4 out of 4 in 3e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3e86. 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 4.68 Na O B:Val64 3.03 Na C B:Val64 4.04 Na N B:Gly65 4.55 Na C B:Gly65 4.80 Na CA B:Gly65 4.18 Na CS B:Cs2 2.59 interactive model: