Sodium in PDB 3pwm: Hiv-1 Protease Mutant L76V with Darunavir

All present enzymatic activity of Hiv-1 Protease Mutant L76V with Darunavir:
3.4.23.16;

The structure of Hiv-1 Protease Mutant L76V with Darunavir, PDB code: 3pwm was solved by Y.Zhang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.46
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.322, 86.329, 45.983, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 18.9

The structure of Hiv-1 Protease Mutant L76V with Darunavir also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hiv-1 Protease Mutant L76V with Darunavir (pdb code 3pwm). 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 L76V with Darunavir, PDB code: 3pwm:

Sodium binding site 1 out of 1 in the Hiv-1 Protease Mutant L76V 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 L76V with Darunavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:26.0 occ:1.00 O A:HOH1090 2.3 10.8 0.5 O A:HOH1203 2.3 39.5 1.0 O A:HOH1089 2.5 22.2 1.0 O A:ASP60 2.5 16.0 1.0 O A:HOH1096 2.6 31.4 1.0 O A:HOH1094 2.8 28.9 1.0 C A:ASP60 3.5 15.1 1.0 N A:ASP60 3.7 13.8 1.0 CA A:ASP60 4.0 15.7 1.0 O A:ARG41 4.2 18.2 1.0 O A:HOH1223 4.3 28.4 0.5 CB A:ASP60 4.3 19.7 1.0 O A:HOH1259 4.4 30.9 0.5 CB A:GLN61 4.5 20.3 1.0 N A:GLN61 4.5 14.1 1.0 N A:ARG41 4.5 23.6 1.0 O A:PRO39 4.6 20.9 1.0 C A:TYR59 4.6 11.7 1.0 CA A:GLY40 4.8 22.1 1.0 CD1 A:ILE62 4.8 15.5 1.0 CA A:GLN61 4.9 15.4 1.0 O A:GLN61 4.9 18.8 1.0 C A:GLN61 4.9 14.8 1.0 OE1 A:GLN61 5.0 44.5 1.0

J.M.Louis, Y.Zhang, J.M.Sayer, Y.F.Wang, R.W.Harrison, I.T.Weber. The L76V Drug Resistance Mutation Decreases the Dimer Stability and Rate of Autoprocessing of Hiv-1 Protease By Reducing Internal Hydrophobic Contacts. Biochemistry V. 50 4786 2011.
ISSN: ISSN 0006-2960
PubMed: 21446746
DOI: 10.1021/BI200033Z