Sodium in the structure of Structure of Human Alpha-Thrombin Y225F Mutant Bound to D-Phe-Pro-Arg- Chloromethylketone (pdb 2thf)

The binding sites of Sodium atom in the structure of Structure of Human Alpha-Thrombin Y225F Mutant Bound to D-Phe-Pro-Arg- Chloromethylketone (pdb code 2thf). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2thf structure was solved by S.CACCIA, K.FUTTERER, E.DI CERA, G.WAKSMAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 6.0-2.1 Space group P212121 a (A) 53.100 b (A) 75.100 c (A) 81.400 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 26.5 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2thf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2thf. 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: Tyr184A, B: Asp221, B: Arg221A, B: Asp222, B: Gly223, B: Lys224, B: Phe225, B: Hoh1604, B: Hoh2191, B: Hoh5037, B: Hoh5217, B: Hoh5269, B: Hoh5359, B: Hoh6310, conact list: Atom Atom Distance (A) Na O B:Tyr184A 4.11 Na O B:Asp221 4.30 Na C B:Asp221 3.93 Na OD1 B:Asp221 4.58 Na CA B:Asp221 4.33 Na O B:Arg221A 2.44 Na N B:Arg221A 3.84 Na C B:Arg221A 3.32 Na CA B:Arg221A 4.21 Na N B:Asp222 4.06 Na C B:Asp222 4.37 Na CA B:Asp222 4.10 Na N B:Gly223 4.31 Na C B:Gly223 4.84 Na O B:Lys224 2.53 Na N B:Lys224 3.80 Na CB B:Lys224 4.39 Na C B:Lys224 3.53 Na CA B:Lys224 4.12 Na N B:Phe225 4.57 Na CA B:Phe225 4.89 Na O B:Hoh1604 2.52 Na O B:Hoh2191 2.63 Na O B:Hoh5037 2.75 Na O B:Hoh5217 4.30 Na O B:Hoh5269 2.85 Na O B:Hoh5359 3.95 Na O B:Hoh6310 4.67 interactive model: