Sodium in the structure of Thrombin in Complex With Inhibitor (pdb 2pks)

The binding sites of Sodium atom in the structure of Thrombin in Complex With Inhibitor (pdb code 2pks). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2pks structure was solved by Y.XUE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 69.7-2.5 Space group C121 a (A) 69.942 b (A) 71.843 c (A) 70.778 alpha (°) 90.00 beta (°) 100.23 gamma (°) 90.00 Rfactor (%) 18.5 Rfree (%) 25.9 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2pks Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2pks. 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: Tyr220, C: Gly228, C: Asp229, C: Asp262, C: Arg263, C: Asp264, C: Lys266, C: Tyr267, C: Hoh406, C: Hoh410, C: Hoh413, conact list: Atom Atom Distance (A) Na O C:Tyr220 4.66 Na O C:Gly228 4.81 Na CB C:Asp229 4.92 Na OD1 C:Asp229 4.65 Na CG C:Asp229 4.86 Na N C:Asp262 4.55 Na C C:Asp262 4.13 Na OD1 C:Asp262 4.28 Na CA C:Asp262 4.04 Na O C:Arg263 2.78 Na N C:Arg263 3.73 Na C C:Arg263 3.81 Na CA C:Arg263 4.41 Na N C:Asp264 4.84 Na O C:Lys266 2.65 Na N C:Lys266 4.51 Na CB C:Lys266 4.48 Na C C:Lys266 3.50 Na CA C:Lys266 4.36 Na N C:Tyr267 4.22 Na CA C:Tyr267 4.28 Na O C:Hoh406 2.88 Na O C:Hoh410 4.76 Na O C:Hoh413 2.84 interactive model: