Sodium in PDB 3djk: Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A

All present enzymatic activity of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A:
3.4.23.16;

The structure of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A, PDB code: 3djk was solved by Y.F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.956, 86.411, 46.029, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.5

The structure of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A (pdb code 3djk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A, PDB code: 3djk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:14.4 occ:1.00 O A:HOH1057 2.3 13.6 1.0 O A:ASP60 2.4 10.7 1.0 O A:HOH1060 2.4 25.2 1.0 O A:HOH1058 2.4 17.3 1.0 O A:HOH1056 2.4 15.3 1.0 O A:HOH1059 2.7 19.6 1.0 C A:ASP60 3.4 9.8 1.0 N A:ASP60 3.8 9.5 1.0 CA A:ASP60 4.0 10.0 1.0 O A:ARG41 4.2 11.5 1.0 O A:HOH1110 4.3 23.8 1.0 O A:HOH1162 4.4 28.5 0.5 CB A:GLN61 4.4 13.6 1.0 CB A:ASP60 4.4 11.8 1.0 N A:ARG41 4.4 14.8 1.0 N A:GLN61 4.4 10.3 1.0 O A:HOH1189 4.5 23.6 0.5 O A:GLN61 4.6 12.9 1.0 CD1 A:ILE62 4.7 12.7 1.0 O A:PRO39 4.7 14.4 1.0 C A:TYR59 4.7 8.5 1.0 CA A:GLN61 4.7 11.1 1.0 O A:HOH1144 4.7 29.1 0.5 C A:GLN61 4.7 10.6 1.0 CA A:GLY40 4.8 16.6 1.0 NE2 A:GLN61 4.9 32.1 1.0 C A:GLY40 5.0 14.9 1.0

Sodium binding site 2 out of 2 in the Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-0255A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:22.6 occ:0.50 O B:HOH1062 2.3 17.1 0.5 O B:HOH1063 2.3 17.5 0.5 O B:HOH1061 2.4 24.4 0.5 O B:HOH1065 2.6 18.6 0.2 O B:HOH1045 2.6 14.7 1.0 O B:HOH1064 2.8 24.8 0.2 OH B:TYR159 3.8 13.1 1.0 CA B:SER137 4.1 17.7 1.0 O B:LEU138 4.2 12.8 1.0 O B:HOH1019 4.2 14.9 1.0 N B:LEU138 4.2 12.7 1.0 NH2 B:ARG157 4.3 18.9 1.0 OG B:SER137 4.3 21.9 0.6 OG B:SER137 4.4 26.1 0.4 CB B:SER137 4.5 21.1 0.4 O B:MET136 4.6 16.8 1.0 CB B:SER137 4.6 20.8 0.6 C B:SER137 4.7 14.4 1.0 CZ B:TYR159 4.9 11.5 1.0

A.K.Ghosh, S.Gemma, A.Baldridge, Y.F.Wang, A.Y.Kovalevsky, Y.Koh, I.T.Weber, H.Mitsuya. Flexible Cyclic Ethers/Polyethers As Novel P2-Ligands For Hiv-1 Protease Inhibitors: Design, Synthesis, Biological Evaluation, and Protein-Ligand X-Ray Studies J.Med.Chem. V. 51 6021 2008.
ISSN: ISSN 0022-2623
PubMed: 18783203
DOI: 10.1021/JM8004543