Sodium in PDB 3ok9: Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A

All present enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A:
3.4.23.16;

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A, PDB code: 3ok9 was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.546, 86.212, 45.635, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.9

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A (pdb code 3ok9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A, PDB code: 3ok9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:31.1 occ:0.50 O A:HOH1107 2.2 32.7 1.0 O A:HOH1108 2.4 24.3 0.5 O A:ASP60 2.5 18.0 1.0 O A:HOH1170 2.7 17.8 0.2 C A:ASP60 3.5 15.8 1.0 N A:ASP60 3.7 16.6 1.0 O A:HOH1047 3.9 33.1 1.0 CA A:ASP60 4.0 16.0 1.0 O A:ARG41 4.3 18.1 1.0 CB A:ASP60 4.3 19.0 1.0 O A:PRO39 4.6 19.8 1.0 N A:GLN61 4.6 16.0 1.0 C A:TYR59 4.6 14.8 1.0 CB A:GLN61 4.7 19.7 1.0 CD1 A:ILE62 4.7 18.9 1.0 C A:GLN61 4.9 16.8 1.0 O A:GLN61 4.9 20.9 1.0 CA A:GLN61 4.9 16.4 1.0 CA A:TYR59 4.9 14.1 1.0 CA A:GLY40 5.0 18.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:26.3 occ:1.00 O B:ASP160 2.3 17.6 1.0 O B:HOH1003 2.3 26.1 1.0 O B:HOH1002 2.4 26.0 1.0 O B:HOH1006 2.5 23.0 0.5 O B:HOH1004 2.5 23.5 1.0 O B:HOH1005 2.8 28.6 0.8 C B:ASP160 3.3 16.1 1.0 N B:ASP160 3.7 16.5 1.0 CA B:ASP160 4.0 16.0 1.0 O B:HOH1126 4.0 26.7 0.5 O B:ARG141 4.2 20.8 1.0 CB B:ASP160 4.3 19.0 1.0 N B:GLN161 4.4 16.4 1.0 CB B:GLN161 4.4 19.8 1.0 N B:ARG141 4.5 28.1 1.0 CD1 B:ILE162 4.6 17.7 1.0 O B:GLN161 4.6 20.6 1.0 O B:PRO139 4.6 27.6 1.0 C B:TYR159 4.6 13.5 1.0 CA B:GLN161 4.8 17.1 1.0 C B:GLN161 4.8 16.6 1.0 CA B:GLY140 4.8 28.4 1.0

A.K.Ghosh, C.X.Xu, K.V.Rao, A.Baldridge, J.Agniswamy, Y.F.Wang, I.T.Weber, M.Aoki, S.G.Miguel, M.Amano, H.Mitsuya. Probing Multidrug-Resistance and Protein-Ligand Interactions with Oxatricyclic Designed Ligands in Hiv-1 Protease Inhibitors. Chemmedchem V. 5 1850 2010.
ISSN: ISSN 1860-7179
PubMed: 20827746
DOI: 10.1002/CMDC.201000318