Sodium in PDB 3jvy: Hiv-1 Protease Mutant G86A with Darunavir

All present enzymatic activity of Hiv-1 Protease Mutant G86A with Darunavir:
3.4.23.16;

The structure of Hiv-1 Protease Mutant G86A with Darunavir, PDB code: 3jvy was solved by Y.Tie, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.328, 86.433, 46.204, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 25.6

The structure of Hiv-1 Protease Mutant G86A with Darunavir also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hiv-1 Protease Mutant G86A with Darunavir (pdb code 3jvy). 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-1 Protease Mutant G86A with Darunavir, PDB code: 3jvy:

Sodium binding site 1 out of 1 in the Hiv-1 Protease Mutant G86A with Darunavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Protease Mutant G86A with Darunavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:30.5 occ:1.00 O A:HOH1074 2.3 26.6 1.0 O A:HOH1079 2.4 30.7 1.0 O A:ASP60 2.4 21.9 1.0 O A:HOH1073 2.6 28.9 1.0 O A:HOH1082 2.9 39.4 1.0 C A:ASP60 3.4 19.6 1.0 N A:ASP60 3.8 19.2 1.0 CA A:ASP60 4.1 21.7 1.0 O A:ARG41 4.3 25.3 1.0 CB A:GLN61 4.4 24.9 1.0 CB A:ASP60 4.4 21.4 1.0 N A:GLN61 4.5 18.2 1.0 O A:PRO39 4.5 27.6 1.0 N A:ARG41 4.6 27.0 1.0 CD1 A:ILE62 4.7 21.6 1.0 CA A:GLY40 4.7 29.1 1.0 C A:TYR59 4.7 14.8 1.0 O A:GLN61 4.8 26.4 1.0 CA A:GLN61 4.8 18.2 1.0 C A:GLN61 4.8 19.1 1.0

R.Ishima, Q.Gong, Y.Tie, I.T.Weber, J.M.Louis. Highly Conserved Glycine 86 and Arginine 87 Residues Contribute Differently to the Structure and Activity of the Mature Hiv-1 Protease Proteins V. 78 1015 2009.
ISSN: ISSN 0887-3585
PubMed: 19899162
DOI: 10.1002/PROT.22625