Sodium in the structure of Crystal Structure Of the Px Domain of Sorting Nexin-17 (SNX17) (pdb 3fog)

The binding sites of Sodium atom in the structure of Crystal Structure Of the Px Domain of Sorting Nexin-17 (SNX17) (pdb code 3fog). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3fog structure was solved by M.WISNIEWSKA, L.TRESAUGUES, C.H.ARROWSMITH, H.BERGLUND, C.BOUNTRA, R.COLLINS, L.G.DAHLGREN, A.M.EDWARDS, S.FLODIN, A.FLORES, S.GRASLUND, M.HAMMARSTROM, A.JOHANSSON, I.JOHANSSON, T.KARLBERG, T.KOTENYOVA, L.LEHTIO, M.MOCHE, M.E.NILSSON, P.NORDLUND, T.NYMAN, C.PERSSON, J.SAGEMARK, M.I.SIPONEN, A.G.THORSELL, S.VAN DEN BERG, J.WEIGELT, M.WELIN, M.WIKSTROM, H.SCHUELER, STRUCTURAL GENOMICS CONSORTIUM (SGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.4-2.8 Space group P321 a (A) 89.890 b (A) 89.890 c (A) 39.260 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23 Rfree (%) 27.9 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3fog Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3fog. 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: Tyr20, A: Arg36, A: Tyr37, A: Ser38, conact list: Atom Atom Distance (A) Na CB A:Tyr20 4.94 Na CB A:Arg36 4.09 Na CD A:Arg36 4.68 Na CZ A:Arg36 3.92 Na C A:Arg36 4.61 Na CG A:Arg36 4.68 Na NE A:Arg36 3.50 Na NH2 A:Arg36 3.40 Na CA A:Arg36 4.91 Na N A:Tyr37 3.94 Na CB A:Tyr37 4.15 Na CD2 A:Tyr37 4.93 Na C A:Tyr37 4.39 Na CA A:Tyr37 4.35 Na N A:Ser38 3.50 Na CB A:Ser38 3.84 Na OG A:Ser38 3.63 Na CA A:Ser38 4.27 interactive model: