Sodium in the structure of Hiv-1 Protease Mutant D30N With Potent Antiviral Inhibitor Grl-98065 (pdb 2qci)

The binding sites of Sodium atom in the structure of Hiv-1 Protease Mutant D30N With Potent Antiviral Inhibitor Grl-98065 (pdb code 2qci). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2qci 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) 10.0-1.2 Space group P21212 a (A) 58.420 b (A) 86.231 c (A) 46.008 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16 Rfree (%) 19.6 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2qci Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2qci. 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: Hoh515, A: Hoh524, A: Hoh530, A: Hoh533, A: Hoh547, A: Hoh565, A: Hoh573, conact list: Atom Atom Distance (A) Na O A:Pro39 4.69 Na C A:Gly40 4.98 Na CA A:Gly40 4.77 Na O A:Arg41 4.17 Na N A:Arg41 4.43 Na C A:Tyr59 4.69 Na O A:Asp60 2.38 Na N A:Asp60 3.73 Na CB A:Asp60 4.35 Na C A:Asp60 3.40 Na CA A:Asp60 4.01 Na O A:Gln61 4.63 Na N A:Gln61 4.46 Na OE1 A:Gln61 4.94 Na CB A:Gln61 4.50 Na C A:Gln61 4.79 Na CA A:Gln61 4.81 Na CD1 A:Ile62 4.58 Na O A:Hoh515 2.41 Na O A:Hoh524 2.41 Na O A:Hoh530 2.66 Na O A:Hoh533 2.33 Na O A:Hoh547 2.42 Na O A:Hoh565 4.18 Na O A:Hoh573 4.24 interactive model: