Sodium in the structure of Hiv-1 Protease Mutant I50V With Potent Antiviral Inhibitor Grl-98065 (pdb 2qd6)

The binding sites of Sodium atom in the structure of Hiv-1 Protease Mutant I50V With Potent Antiviral Inhibitor Grl-98065 (pdb code 2qd6). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2qd6 structure was solved by Y.F.WANG, Y.TIE, P.I.BOROSS, J.TOZSER, A.K.GHOSH, R.W.HARRISON, I.T.WEBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.3 Space group P21212 a (A) 58.294 b (A) 86.228 c (A) 46.006 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.5 Rfree (%) 20.2 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2qd6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2qd6. 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: Hoh512, A: Hoh521, A: Hoh530, A: Hoh533, A: Hoh549, conact list: Atom Atom Distance (A) Na O A:Pro39 4.63 Na CA A:Gly40 4.73 Na O A:Arg41 4.18 Na N A:Arg41 4.51 Na C A:Tyr59 4.68 Na O A:Asp60 2.35 Na N A:Asp60 3.74 Na CB A:Asp60 4.37 Na C A:Asp60 3.37 Na CA A:Asp60 4.00 Na O A:Gln61 4.65 Na N A:Gln61 4.42 Na OE1 A:Gln61 4.81 Na CB A:Gln61 4.40 Na C A:Gln61 4.79 Na CA A:Gln61 4.76 Na CD1 A:Ile62 4.73 Na O A:Hoh512 2.35 Na O A:Hoh521 2.35 Na O A:Hoh530 2.80 Na O A:Hoh533 2.22 Na O A:Hoh549 2.51 interactive model: