Sodium in the structure of Wild Type Hiv-1 Protease With Antiviral Drug Amprenavir (pdb 3nu3)

The binding sites of Sodium atom in the structure of Wild Type Hiv-1 Protease With Antiviral Drug Amprenavir (pdb code 3nu3). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3nu3 structure was solved by Y.-F.WANG, A.Y.KOVALEVSKY, I.T.WEBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.0 Space group P21212 a (A) 58.107 b (A) 85.971 c (A) 46.420 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 12.3 Rfree (%) 14.2 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3nu3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3nu3. 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: Hoh1128, A: Hoh1129, A: Hoh1130, A: Hoh1131, A: Hoh1132, conact list: Atom Atom Distance (A) Na O A:Pro39 4.49 Na C A:Gly40 4.96 Na CA A:Gly40 4.63 Na O A:Arg41 4.29 Na N A:Arg41 4.54 Na C A:Tyr59 4.73 Na O A:Asp60 2.42 Na N A:Asp60 3.73 Na CB A:Asp60 4.27 Na C A:Asp60 3.34 Na CA A:Asp60 3.94 Na O A:Gln61 4.60 Na O A:Gln61 4.94 Na N A:Gln61 4.40 Na N A:Gln61 4.38 Na OE1 A:Gln61 4.14 Na OE1 A:Gln61 4.85 Na CB A:Gln61 4.23 Na CB A:Gln61 4.29 Na CD A:Gln61 4.78 Na C A:Gln61 4.76 Na C A:Gln61 4.89 Na CA A:Gln61 4.69 Na CA A:Gln61 4.73 Na CD1 A:Ile62 4.82 Na O A:Hoh1128 2.29 Na O A:Hoh1129 2.33 Na O A:Hoh1130 2.41 Na O A:Hoh1131 2.32 Na O A:Hoh1132 2.76 interactive model: