Sodium in the structure of Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-0255A (pdb 3djk)

The binding sites of Sodium atom in the structure of Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-0255A (pdb code 3djk). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3djk structure was solved by Y.F.WANG, 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) 57.956 b (A) 86.411 c (A) 46.029 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 14.7 Rfree (%) 17.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 3djk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3djk. 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: Hoh1056, A: Hoh1057, A: Hoh1058, A: Hoh1059, A: Hoh1060, A: Hoh1110, A: Hoh1144, A: Hoh1162, A: Hoh1189, conact list: Atom Atom Distance (A) Na O A:Pro39 4.71 Na C A:Gly40 4.99 Na CA A:Gly40 4.78 Na O A:Arg41 4.17 Na N A:Arg41 4.42 Na C A:Tyr59 4.73 Na O A:Asp60 2.36 Na N A:Asp60 3.77 Na CB A:Asp60 4.39 Na C A:Asp60 3.38 Na CA A:Asp60 4.02 Na O A:Gln61 4.58 Na NE2 A:Gln61 4.92 Na N A:Gln61 4.43 Na CB A:Gln61 4.38 Na C A:Gln61 4.74 Na CA A:Gln61 4.73 Na CD1 A:Ile62 4.69 Na O A:Hoh1056 2.42 Na O A:Hoh1057 2.32 Na O A:Hoh1058 2.41 Na O A:Hoh1059 2.68 Na O A:Hoh1060 2.38 Na O A:Hoh1110 4.29 Na O A:Hoh1144 4.74 Na O A:Hoh1162 4.36 Na O A:Hoh1189 4.53 interactive model: Sodium binding site 2 out of 2 in 3djk Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3djk. 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: Met136, B: Ser137, B: Leu138, B: Arg157, B: Tyr159, B: Hoh1019, B: Hoh1045, B: Hoh1061, B: Hoh1062, B: Hoh1063, B: Hoh1064, B: Hoh1065, conact list: Atom Atom Distance (A) Na O B:Met136 4.62 Na CB B:Ser137 4.65 Na CB B:Ser137 4.52 Na OG B:Ser137 4.35 Na OG B:Ser137 4.40 Na C B:Ser137 4.74 Na CA B:Ser137 4.15 Na O B:Leu138 4.15 Na N B:Leu138 4.24 Na NH2 B:Arg157 4.32 Na CZ B:Tyr159 4.87 Na OH B:Tyr159 3.82 Na O B:Hoh1019 4.17 Na O B:Hoh1045 2.64 Na O B:Hoh1061 2.35 Na O B:Hoh1062 2.26 Na O B:Hoh1063 2.34 Na O B:Hoh1064 2.76 Na O B:Hoh1065 2.64 interactive model: