Sodium in PDB 8esx: Hiv Protease in Complex with Benzoxaborolone Analog of Darunavir

The structure of Hiv Protease in Complex with Benzoxaborolone Analog of Darunavir, PDB code: 8esx was solved by I.W.Windsor, B.J.Graham, R.T.Raines, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.10 / 1.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.97, 86.31, 45.94, 90, 90, 90
R / Rfree (%)	18.3 / 20.6

The structure of Hiv Protease in Complex with Benzoxaborolone Analog of Darunavir also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Hiv Protease in Complex with Benzoxaborolone Analog of Darunavir (pdb code 8esx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hiv Protease in Complex with Benzoxaborolone Analog of Darunavir, PDB code: 8esx:

Sodium binding site 1 out of 1 in the Hiv Protease in Complex with Benzoxaborolone Analog of Darunavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv Protease in Complex with Benzoxaborolone Analog of Darunavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:25.1 occ:1.00 O A:HOH219 2.3 26.4 1.0 O A:ASP60 2.3 19.3 1.0 O A:HOH252 2.4 30.7 1.0 O A:HOH225 2.5 36.4 1.0 O A:HOH214 2.5 25.9 1.0 O A:HOH257 2.8 31.6 1.0 C A:ASP60 3.3 17.6 1.0 N A:ASP60 3.7 18.1 1.0 CA A:ASP60 4.0 18.8 1.0 O A:ARG41 4.2 23.2 1.0 CB A:ASP60 4.4 22.2 1.0 N A:GLN61 4.4 18.1 1.0 CB A:GLN61 4.5 23.2 1.0 O A:GLN61 4.6 21.6 1.0 O A:PRO39 4.6 24.3 1.0 N A:ARG41 4.6 22.4 1.0 C A:TYR59 4.7 16.9 1.0 NE2 A:GLN61 4.7 47.9 1.0 CD1 A:ILE62 4.7 20.4 1.0 CA A:GLN61 4.7 20.2 1.0 C A:GLN61 4.7 19.1 1.0 CA A:GLY40 4.8 25.9 1.0 O A:HOH216 4.8 41.0 1.0 CG A:GLN61 4.9 27.8 1.0

B.J.Graham, I.W.Windsor, R.T.Raines. Inhibition of Hiv-1 Protease By A Boronic Acid with High Oxidative Stability Acs Med.Chem.Lett. 2023.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.2C00464