Sodium in the structure of Crystal Structure of Wild Type Hiv-1 Protease With Macrocyclic Inhibitor Grl-0216A (pdb 3i6o)

The binding sites of Sodium atom in the structure of Crystal Structure of Wild Type Hiv-1 Protease With Macrocyclic Inhibitor Grl-0216A (pdb code 3i6o). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3i6o structure was solved by A.A.CHUMANEVICH, 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) 10.0-1.2 Space group P21212 a (A) 58.764 b (A) 86.328 c (A) 45.976 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.9 Rfree (%) 19.6 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3i6o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3i6o. 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: Hoh1023, A: Hoh1055, A: Hoh1076, A: Hoh1094, A: Hoh1107, A: Hoh1139, conact list: Atom Atom Distance (A) Na O A:Pro39 4.65 Na C A:Gly40 4.99 Na CA A:Gly40 4.82 Na O A:Arg41 4.08 Na N A:Arg41 4.38 Na C A:Tyr59 4.73 Na O A:Asp60 2.44 Na N A:Asp60 3.78 Na CB A:Asp60 4.38 Na C A:Asp60 3.44 Na CA A:Asp60 4.04 Na O A:Gln61 4.66 Na N A:Gln61 4.48 Na OE1 A:Gln61 4.89 Na CB A:Gln61 4.44 Na C A:Gln61 4.83 Na CA A:Gln61 4.82 Na CD1 A:Ile62 4.72 Na O A:Hoh1023 2.31 Na O A:Hoh1055 2.46 Na O A:Hoh1076 2.49 Na O A:Hoh1094 2.60 Na O A:Hoh1107 2.34 Na O A:Hoh1139 4.67 interactive model: Sodium binding site 2 out of 2 in 3i6o Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3i6o. 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: Pro139, B: Gly140, B: Arg141, B: Tyr159, B: Asp160, B: Gln161, B: Ile162, B: Hoh1034, B: Hoh1048, B: Hoh1068, B: Hoh1069, B: Hoh1098, conact list: Atom Atom Distance (A) Na O B:Pro139 4.41 Na C B:Gly140 5.00 Na CA B:Gly140 4.67 Na O B:Arg141 4.05 Na N B:Arg141 4.54 Na C B:Tyr159 4.64 Na CA B:Tyr159 4.95 Na O B:Asp160 2.46 Na N B:Asp160 3.71 Na CB B:Asp160 4.38 Na C B:Asp160 3.48 Na CA B:Asp160 4.02 Na O B:Gln161 4.83 Na N B:Gln161 4.59 Na CB B:Gln161 4.80 Na CB B:Gln161 4.23 Na C B:Gln161 4.91 Na CA B:Gln161 4.97 Na CA B:Gln161 4.82 Na CD1 B:Ile162 4.74 Na O B:Hoh1034 2.26 Na O B:Hoh1048 2.45 Na O B:Hoh1068 2.71 Na O B:Hoh1069 2.35 Na O B:Hoh1098 2.55 interactive model: