Sodium in PDB 3nu3: Wild Type Hiv-1 Protease with Antiviral Drug Amprenavir

All present enzymatic activity of Wild Type Hiv-1 Protease with Antiviral Drug Amprenavir:
3.4.23.16;

The structure of Wild Type Hiv-1 Protease with Antiviral Drug Amprenavir, PDB code: 3nu3 was solved by Y.-F.Wang, A.Y.Kovalevsky, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.02
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.107, 85.971, 46.420, 90.00, 90.00, 90.00
R / Rfree (%)	12.3 / 14.2

The structure of Wild Type Hiv-1 Protease with Antiviral Drug Amprenavir also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Wild Type Hiv-1 Protease with Antiviral Drug Amprenavir (pdb code 3nu3). 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 Wild Type Hiv-1 Protease with Antiviral Drug Amprenavir, PDB code: 3nu3:

Sodium binding site 1 out of 1 in the Wild Type Hiv-1 Protease with Antiviral Drug Amprenavir


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 Antiviral Drug Amprenavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:25.8 occ:1.00 O A:HOH1128 2.3 24.4 1.0 O A:HOH1131 2.3 23.6 0.5 O A:HOH1129 2.3 24.5 1.0 O A:HOH1130 2.4 17.0 0.5 O A:ASP60 2.4 13.8 1.0 O A:HOH1132 2.8 26.7 0.5 C A:ASP60 3.3 12.7 1.0 N A:ASP60 3.7 12.2 1.0 CA A:ASP60 3.9 12.8 1.0 OE1 A:GLN61 4.1 34.9 0.5 CB A:GLN61 4.2 18.6 0.5 CB A:ASP60 4.3 14.7 1.0 CB A:GLN61 4.3 18.0 0.5 O A:ARG41 4.3 16.5 1.0 N A:GLN61 4.4 13.0 0.5 N A:GLN61 4.4 13.0 0.5 O A:PRO39 4.5 18.2 1.0 N A:ARG41 4.5 18.0 1.0 O A:GLN61 4.6 15.8 0.5 CA A:GLY40 4.6 19.3 1.0 CA A:GLN61 4.7 13.7 0.5 C A:TYR59 4.7 9.6 1.0 CA A:GLN61 4.7 13.8 0.5 C A:GLN61 4.8 12.1 0.5 CD A:GLN61 4.8 25.2 0.5 CD1 A:ILE62 4.8 12.2 1.0 OE1 A:GLN61 4.8 30.8 0.5 C A:GLN61 4.9 12.3 0.5 O A:GLN61 4.9 16.1 0.5 C A:GLY40 5.0 16.5 1.0

C.H.Shen, Y.F.Wang, A.Y.Kovalevsky, R.W.Harrison, I.T.Weber. Amprenavir Complexes with Hiv-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters. Febs J. V. 277 3699 2010.
ISSN: ISSN 1742-464X
PubMed: 20695887
DOI: 10.1111/J.1742-4658.2010.07771.X