Sodium in the structure of Factor Xa in Complex With A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor (pdb 2xby)

The binding sites of Sodium atom in the structure of Factor Xa in Complex With A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor (pdb code 2xby). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2xby structure was solved by D.W.BANNER, J.BENZ, D.SCHLATTER, S.THOMI, W.HAAP, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 14.8-2.0 Space group P43212 a (A) 106.640 b (A) 106.640 c (A) 50.900 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21 Rfree (%) 24.6 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2xby Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2xby. 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: Hoh2163, A: Hoh2170, A: Hoh2192, conact list: Atom Atom Distance (A) Na O A:Tyr185 2.40 Na C A:Tyr185 3.52 Na CA A:Tyr185 4.75 Na O A:Asp185A 2.66 Na N A:Asp185A 4.09 Na C A:Asp185A 3.29 Na CA A:Asp185A 3.81 Na N A:Thr185B 4.15 Na CA A:Thr185B 4.57 Na O A:Lys186 4.67 Na O A:Ala221 4.22 Na C A:Ala221 4.05 Na CA A:Ala221 4.59 Na O A:Arg222 2.23 Na N A:Arg222 4.05 Na C A:Arg222 3.32 Na CA A:Arg222 4.29 Na N A:Lys223 4.12 Na C A:Lys223 4.41 Na CA A:Lys223 4.14 Na N A:Gly223A 4.15 Na C A:Gly223A 4.78 Na O A:Lys224 2.46 Na N A:Lys224 3.73 Na CB A:Lys224 4.79 Na C A:Lys224 3.60 Na CA A:Lys224 4.21 Na N A:Tyr225 4.70 Na CA A:Tyr225 5.00 Na O A:Hoh2163 4.42 Na O A:Hoh2170 2.47 Na O A:Hoh2192 2.83 interactive model: