Sodium in the structure of Crystal Structure of Hiv Protease Model Precursor/Darunavir Complex (pdb 3tkw)

The binding sites of Sodium atom in the structure of Crystal Structure of Hiv Protease Model Precursor/Darunavir Complex (pdb code 3tkw). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3tkw structure was solved by J.AGNISWAMY, J.SAYER, I.WEBER, J.LOUIS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.6 Space group P21212 a (A) 59.317 b (A) 86.223 c (A) 45.951 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.7 Rfree (%) 23.1 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3tkw Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3tkw. 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: Pro39, A: Gly40, A: Arg41, A: Tyr59, A: Asp60, A: Gln61, A: Ile62, A: Hoh1027, A: Hoh1054, A: Hoh1062, A: Hoh1077, A: Hoh1078, A: Hoh1080, conact list: Atom Atom Distance (A) Na O A:Pro39 4.59 Na CA A:Gly40 4.93 Na O A:Arg41 4.12 Na N A:Arg41 4.46 Na C A:Tyr59 4.73 Na O A:Asp60 2.37 Na N A:Asp60 3.80 Na CB A:Asp60 4.54 Na C A:Asp60 3.43 Na CA A:Asp60 4.09 Na O A:Gln61 4.54 Na N A:Gln61 4.51 Na CB A:Gln61 4.58 Na C A:Gln61 4.70 Na CA A:Gln61 4.83 Na CD1 A:Ile62 4.54 Na O A:Hoh1027 2.61 Na O A:Hoh1054 2.25 Na O A:Hoh1062 2.48 Na O A:Hoh1077 3.88 Na O A:Hoh1078 2.32 Na O A:Hoh1080 2.56 interactive model: