Sodium in the structure of Crystal Structure of E.Coli Gs Mutant E377A in Complex With Adp and Oligosaccharides (pdb 3cx4)

The binding sites of Sodium atom in the structure of Crystal Structure of E.Coli Gs Mutant E377A in Complex With Adp and Oligosaccharides (pdb code 3cx4). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3cx4 structure was solved by F.SHENG, J.H.GEIGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 9.3-2.3 Space group I41 a (A) 126.324 b (A) 126.324 c (A) 152.334 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 22.1 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3cx4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3cx4. 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: Val298, A: Ser299, A: Arg300, A: Lys305, A: Adp500, A: Hoh629, conact list: Atom Atom Distance (A) Na O A:Val298 4.69 Na N A:Ser299 4.85 Na CB A:Ser299 4.53 Na OG A:Ser299 4.17 Na C A:Ser299 3.83 Na CA A:Ser299 3.78 Na O A:Arg300 4.71 Na N A:Arg300 2.96 Na CB A:Arg300 3.65 Na CD A:Arg300 4.15 Na CZ A:Arg300 4.85 Na C A:Arg300 4.83 Na CG A:Arg300 3.52 Na NE A:Arg300 3.83 Na CA A:Arg300 3.87 Na CE A:Lys305 3.93 Na CD A:Lys305 4.81 Na NZ A:Lys305 3.70 Na N9 A:Adp500 4.65 Na PA A:Adp500 4.58 Na C8 A:Adp500 3.55 Na O2A A:Adp500 4.63 Na O1B A:Adp500 4.42 Na PB A:Adp500 3.82 Na N7 A:Adp500 4.23 Na O4' A:Adp500 4.52 Na C5' A:Adp500 3.56 Na C4' A:Adp500 4.70 Na O5' A:Adp500 4.49 Na O2B A:Adp500 2.96 Na O3A A:Adp500 3.62 Na O A:Hoh629 3.08 interactive model: Sodium binding site 2 out of 2 in 3cx4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3cx4. 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: Thr159, A: Thr209, A: Ala210, A: Val211, A: Val244, A: Tyr469, A: Hoh545, conact list: Atom Atom Distance (A) Na CB A:Thr159 4.03 Na CG2 A:Thr159 4.40 Na OG1 A:Thr159 4.06 Na O A:Thr209 4.53 Na CB A:Thr209 3.28 Na CG2 A:Thr209 4.33 Na OG1 A:Thr209 2.57 Na C A:Thr209 4.04 Na CA A:Thr209 4.32 Na O A:Ala210 2.95 Na N A:Ala210 3.89 Na C A:Ala210 3.43 Na CA A:Ala210 4.18 Na N A:Val211 3.97 Na CB A:Val211 4.66 Na C A:Val211 4.89 Na CG1 A:Val211 4.08 Na CA A:Val211 3.91 Na O A:Val244 3.47 Na N A:Val244 3.94 Na CB A:Val244 3.84 Na CG2 A:Val244 4.43 Na C A:Val244 4.28 Na CG1 A:Val244 4.88 Na CA A:Val244 4.24 Na CE2 A:Tyr469 3.67 Na CZ A:Tyr469 3.48 Na CE1 A:Tyr469 4.71 Na OH A:Tyr469 2.53 Na O A:Hoh545 3.90 interactive model: