Sodium in the structure of Crystal Structure Of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel (pdb 3igq)

The binding sites of Sodium atom in the structure of Crystal Structure Of the Extracellular Domain of A Bacterial Pentameric Ligand-Gated Ion Channel (pdb code 3igq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3igq structure was solved by H.NURY, M.DELARUE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.0-2.3 Space group P21212 a (A) 84.450 b (A) 130.240 c (A) 113.590 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.7 Rfree (%) 25.5 Sodium Binding Sites: Sodium binding site 1 out of 6 in 3igq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3igq. 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: Val5, A: Pro68, A: Glu69, A: Ala70, A: Ile71, A: Trp72, A: Ile73, A: Hoh226, A: Hoh237, conact list: Atom Atom Distance (A) Na CG1 A:Val5 4.23 Na O A:Pro68 2.19 Na CB A:Pro68 4.72 Na C A:Pro68 3.36 Na CA A:Pro68 4.32 Na O A:Glu69 4.47 Na N A:Glu69 4.19 Na C A:Glu69 4.32 Na CA A:Glu69 4.12 Na N A:Ala70 4.89 Na O A:Ile71 2.43 Na N A:Ile71 4.38 Na C A:Ile71 3.66 Na CA A:Ile71 4.62 Na N A:Trp72 4.52 Na C A:Trp72 4.51 Na CA A:Trp72 4.46 Na N A:Ile73 4.18 Na CB A:Ile73 4.36 Na CD1 A:Ile73 4.05 Na CG1 A:Ile73 4.05 Na CA A:Ile73 4.92 Na O A:Hoh226 2.33 Na O A:Hoh237 4.86 interactive model: Sodium binding site 2 out of 6 in 3igq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3igq. 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: Val5, B: Pro68, B: Glu69, B: Ile71, B: Trp72, B: Ile73, B: Hoh430, conact list: Atom Atom Distance (A) Na CG1 B:Val5 4.14 Na O B:Pro68 2.38 Na CB B:Pro68 4.96 Na C B:Pro68 3.57 Na CA B:Pro68 4.56 Na O B:Glu69 4.42 Na N B:Glu69 4.37 Na C B:Glu69 4.43 Na CA B:Glu69 4.26 Na O B:Ile71 2.46 Na N B:Ile71 4.54 Na C B:Ile71 3.67 Na CA B:Ile71 4.72 Na N B:Trp72 4.46 Na C B:Trp72 4.53 Na CA B:Trp72 4.33 Na N B:Ile73 4.13 Na CB B:Ile73 4.42 Na CD1 B:Ile73 4.18 Na CG1 B:Ile73 4.16 Na CA B:Ile73 4.92 Na O B:Hoh430 2.38 interactive model: Sodium binding site 3 out of 6 in 3igq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3igq. 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: C: Val5, C: Pro68, C: Glu69, C: Ala70, C: Ile71, C: Trp72, C: Ile73, C: Hoh234, conact list: Atom Atom Distance (A) Na CG1 C:Val5 4.10 Na O C:Pro68 2.36 Na CB C:Pro68 5.00 Na C C:Pro68 3.56 Na CA C:Pro68 4.54 Na O C:Glu69 4.43 Na N C:Glu69 4.37 Na C C:Glu69 4.39 Na CA C:Glu69 4.27 Na N C:Ala70 4.98 Na O C:Ile71 2.24 Na N C:Ile71 4.38 Na C C:Ile71 3.50 Na CA C:Ile71 4.53 Na N C:Trp72 4.34 Na C C:Trp72 4.38 Na CA C:Trp72 4.23 Na N C:Ile73 4.08 Na CB C:Ile73 4.34 Na CD1 C:Ile73 4.19 Na CG1 C:Ile73 3.99 Na CA C:Ile73 4.84 Na O C:Hoh234 2.62 interactive model: Sodium binding site 4 out of 6 in 3igq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3igq. 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: D: Val5, D: Pro68, D: Glu69, D: Ala70, D: Ile71, D: Trp72, D: Ile73, D: Hoh205, D: Hoh225, conact list: Atom Atom Distance (A) Na CG1 D:Val5 3.99 Na O D:Pro68 2.45 Na CB D:Pro68 5.00 Na C D:Pro68 3.62 Na CA D:Pro68 4.60 Na O D:Glu69 4.36 Na N D:Glu69 4.40 Na C D:Glu69 4.35 Na CA D:Glu69 4.24 Na N D:Ala70 5.00 Na O D:Ile71 2.40 Na N D:Ile71 4.42 Na C D:Ile71 3.60 Na CA D:Ile71 4.61 Na N D:Trp72 4.42 Na C D:Trp72 4.55 Na CA D:Trp72 4.35 Na N D:Ile73 4.19 Na CB D:Ile73 4.44 Na CD1 D:Ile73 4.19 Na CG1 D:Ile73 4.19 Na CA D:Ile73 4.95 Na O D:Hoh205 2.43 Na O D:Hoh225 4.93 interactive model: Sodium binding site 5 out of 6 in 3igq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3igq. 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: E: Val5, E: Pro68, E: Glu69, E: Ala70, E: Ile71, E: Trp72, E: Ile73, E: Hoh403, conact list: Atom Atom Distance (A) Na CG1 E:Val5 4.25 Na O E:Pro68 2.13 Na CB E:Pro68 4.81 Na C E:Pro68 3.31 Na CA E:Pro68 4.30 Na O E:Glu69 4.35 Na N E:Glu69 4.11 Na C E:Glu69 4.18 Na CA E:Glu69 4.05 Na N E:Ala70 4.71 Na O E:Ile71 2.27 Na N E:Ile71 4.22 Na C E:Ile71 3.47 Na CA E:Ile71 4.43 Na N E:Trp72 4.33 Na C E:Trp72 4.49 Na CA E:Trp72 4.34 Na N E:Ile73 4.22 Na CB E:Ile73 4.46 Na CD1 E:Ile73 4.02 Na CG1 E:Ile73 4.02 Na CA E:Ile73 4.99 Na O E:Hoh403 2.27 interactive model: Sodium binding site 6 out of 6 in 3igq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3igq. 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: F: Val5, F: Pro68, F: Glu69, F: Ala70, F: Ile71, F: Trp72, F: Ile73, F: Hoh208, F: Hoh237, F: Hoh245, conact list: Atom Atom Distance (A) Na CG1 F:Val5 4.13 Na O F:Pro68 2.35 Na CB F:Pro68 4.92 Na C F:Pro68 3.50 Na CA F:Pro68 4.48 Na O F:Glu69 4.48 Na N F:Glu69 4.31 Na C F:Glu69 4.38 Na CA F:Glu69 4.24 Na N F:Ala70 4.99 Na O F:Ile71 2.34 Na N F:Ile71 4.46 Na C F:Ile71 3.57 Na CA F:Ile71 4.62 Na N F:Trp72 4.37 Na C F:Trp72 4.44 Na CA F:Trp72 4.29 Na N F:Ile73 4.07 Na CB F:Ile73 4.29 Na CD1 F:Ile73 4.11 Na CG1 F:Ile73 4.03 Na CA F:Ile73 4.82 Na O F:Hoh208 4.82 Na O F:Hoh237 2.62 Na O F:Hoh245 2.46 interactive model: