Sodium in PDB 6o48: Wild-Type Hiv-1 Protease in Complex with A Substrate Analog Ca-P2

The structure of Wild-Type Hiv-1 Protease in Complex with A Substrate Analog Ca-P2, PDB code: 6o48 was solved by Y.-F.Wang, F.Liu, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.46
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.407, 86.244, 46.581, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.5

The structure of Wild-Type Hiv-1 Protease in Complex with A Substrate Analog Ca-P2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Wild-Type Hiv-1 Protease in Complex with A Substrate Analog Ca-P2 (pdb code 6o48). 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 in Complex with A Substrate Analog Ca-P2, PDB code: 6o48:

Sodium binding site 1 out of 1 in the Wild-Type Hiv-1 Protease in Complex with A Substrate Analog Ca-P2


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 in Complex with A Substrate Analog Ca-P2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:18.5 occ:0.75 O A:HOH621 2.2 23.2 1.0 O A:HOH639 2.3 29.2 1.0 O A:HOH619 2.4 22.8 1.0 O A:ASP60 2.4 15.9 1.0 O A:HOH626 2.5 32.5 1.0 O A:HOH630 3.0 39.4 1.0 C A:ASP60 3.4 15.4 1.0 N A:ASP60 3.6 14.1 1.0 CA A:ASP60 4.0 15.7 1.0 O A:ARG41 4.2 18.5 1.0 CB A:ASP60 4.4 18.5 1.0 N A:GLN61 4.5 16.0 1.0 O A:PRO39 4.5 21.3 1.0 CB A:GLN61 4.6 19.9 1.0 N A:ARG41 4.6 21.0 1.0 CD1 A:ILE62 4.6 16.9 1.0 C A:TYR59 4.6 12.1 1.0 O A:GLN61 4.7 19.3 1.0 CA A:GLY40 4.7 22.0 1.0 C A:GLN61 4.8 16.0 1.0 CA A:GLN61 4.9 16.0 1.0

J.Agniswamy, D.W.Kneller, R.Brothers, Y.F.Wang, R.W.Harrison, I.T.Weber. Highly Drug-Resistant Hiv-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues. Acs Omega V. 4 8707 2019.
ISSN: ESSN 2470-1343
PubMed: 31172041
DOI: 10.1021/ACSOMEGA.9B00683