Sodium in the structure of Aminopyrrolidine Factor Xa Inhibitor (pdb 2vwn)

The binding sites of Sodium atom in the structure of Aminopyrrolidine Factor Xa Inhibitor (pdb code 2vwn). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2vwn structure was solved by K.GROEBKE-ZBINDEN, D.W.BANNER, J.M.BENZ, F.BLASCO, G.DECORET, J.HIMBER, B.KUHN, N.PANDAY, F.RICKLIN, P.RISCH, D.SCHLATTER, M.STAHL, R.UNGER, W.HAAP, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 74.5-1.6 Space group P43212 a (A) 105.540 b (A) 105.540 c (A) 49.790 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.1 Rfree (%) 22.8 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2vwn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2vwn. 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: Tyr185, A: Asp185A, A: Thr185B, A: Lys186, A: Ala221, A: Arg222, A: Lys223, A: Gly223A, A: Lys224, A: Tyr225, A: Hoh2184, A: Hoh2188, A: Hoh2205, conact list: Atom Atom Distance (A) Na O A:Tyr185 2.28 Na N A:Tyr185 4.90 Na C A:Tyr185 3.45 Na CA A:Tyr185 4.65 Na O A:Asp185A 2.30 Na N A:Asp185A 4.07 Na C A:Asp185A 3.16 Na CA A:Asp185A 3.78 Na N A:Thr185B 4.11 Na C A:Thr185B 4.99 Na CA A:Thr185B 4.55 Na O A:Lys186 4.71 Na O A:Ala221 4.36 Na C A:Ala221 4.09 Na CA A:Ala221 4.53 Na O A:Arg222 2.29 Na N A:Arg222 4.08 Na C A:Arg222 3.40 Na CA A:Arg222 4.38 Na N A:Lys223 4.20 Na C A:Lys223 4.42 Na CA A:Lys223 4.21 Na N A:Gly223A 4.12 Na C A:Gly223A 4.72 Na CA A:Gly223A 4.90 Na O A:Lys224 2.26 Na O A:Lys224 2.26 Na N A:Lys224 3.66 Na N A:Lys224 3.66 Na CB A:Lys224 4.66 Na CB A:Lys224 4.64 Na C A:Lys224 3.42 Na C A:Lys224 3.42 Na CA A:Lys224 4.09 Na CA A:Lys224 4.08 Na N A:Tyr225 4.52 Na CA A:Tyr225 4.81 Na O A:Hoh2184 2.34 Na O A:Hoh2188 4.47 Na O A:Hoh2205 2.77 interactive model: Sodium binding site 2 out of 2 in 2vwn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2vwn. 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: Met131B, A: Thr132, A: Gln133, A: Tyr162, A: Hoh2045, A: Hoh2046, A: Hoh2057, A: Hoh2119, A: Hoh2121, A: Hoh2123, A: Hoh2148, A: Hoh2151, A: Hoh2152, conact list: Atom Atom Distance (A) Na O A:Met131B 4.43 Na O A:Thr132 4.24 Na C A:Thr132 4.53 Na CA A:Thr132 4.50 Na O A:Gln133 4.33 Na CB A:Tyr162 4.84 Na O A:Hoh2045 2.11 Na O A:Hoh2046 2.38 Na O A:Hoh2057 4.04 Na O A:Hoh2119 2.36 Na O A:Hoh2121 2.23 Na O A:Hoh2123 4.74 Na O A:Hoh2148 2.32 Na O A:Hoh2151 4.26 Na O A:Hoh2152 4.97 interactive model: