Sodium in the structure of Crystal Structure of Human Alpha Thrombin in Complex With Benzo[B]Thiophene Inhibitor 1 (pdb 1d3t)

The binding sites of Sodium atom in the structure of Crystal Structure of Human Alpha Thrombin in Complex With Benzo[B]Thiophene Inhibitor 1 (pdb code 1d3t). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1d3t structure was solved by N.Y.CHIRGADZE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.0 Space group C121 a (A) 71.140 b (A) 71.850 c (A) 72.960 alpha (°) 90.00 beta (°) 100.50 gamma (°) 90.00 Rfactor (%) 17.2 Rfree (%) 23.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 1d3t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1d3t. 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: B: Lys210, B: Asp211, B: Thr213, B: Arg214, conact list: Atom Atom Distance (A) Na O B:Lys210 2.59 Na CB B:Lys210 4.99 Na C B:Lys210 3.65 Na CA B:Lys210 4.67 Na N B:Asp211 4.37 Na C B:Asp211 4.71 Na CA B:Asp211 4.31 Na O B:Thr213 2.42 Na N B:Thr213 4.51 Na CG2 B:Thr213 4.99 Na C B:Thr213 3.64 Na CA B:Thr213 4.65 Na N B:Arg214 4.46 Na C B:Arg214 4.83 Na CA B:Arg214 4.42 interactive model: Sodium binding site 2 out of 2 in 1d3t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1d3t. 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: B: Tyr226, B: Asp235, B: Asp268, B: Arg269, B: Asp270, B: Lys272, B: Tyr273, conact list: Atom Atom Distance (A) Na O B:Tyr226 4.73 Na CB B:Asp235 4.87 Na OD2 B:Asp235 4.65 Na CG B:Asp235 4.92 Na N B:Asp268 4.55 Na C B:Asp268 4.14 Na OD1 B:Asp268 4.55 Na CA B:Asp268 4.02 Na O B:Arg269 2.86 Na N B:Arg269 3.77 Na C B:Arg269 3.95 Na CA B:Arg269 4.54 Na N B:Asp270 4.99 Na O B:Lys272 2.43 Na N B:Lys272 4.26 Na CB B:Lys272 4.52 Na C B:Lys272 3.43 Na CA B:Lys272 4.30 Na N B:Tyr273 4.25 Na CD2 B:Tyr273 4.88 Na CA B:Tyr273 4.26 interactive model: