Sodium in PDB 6dj1: Wild-Type Hiv-1 Protease in Complex with Lopinavir

The structure of Wild-Type Hiv-1 Protease in Complex with Lopinavir, PDB code: 6dj1 was solved by Y.-F.Wang, A.E.Wong-Sam, Y.Zhang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.00 / 1.26
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.726, 85.199, 46.266, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.8

The structure of Wild-Type Hiv-1 Protease in Complex with Lopinavir also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Wild-Type Hiv-1 Protease in Complex with Lopinavir (pdb code 6dj1). 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 Lopinavir, PDB code: 6dj1:

Sodium binding site 1 out of 1 in the Wild-Type Hiv-1 Protease in Complex with Lopinavir


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 Lopinavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:24.4 occ:1.00 O A:HOH642 2.2 29.2 1.0 O A:HOH622 2.3 20.7 1.0 O A:HOH654 2.4 23.6 1.0 O A:ASP60 2.4 16.6 1.0 O A:HOH629 2.4 23.6 1.0 O A:HOH660 2.7 32.7 1.0 C A:ASP60 3.4 14.9 1.0 N A:ASP60 3.8 15.5 1.0 CA A:ASP60 4.0 15.4 1.0 O A:ARG41 4.2 20.1 1.0 CB A:GLN61 4.4 19.2 1.0 CB A:ASP60 4.4 16.1 1.0 N A:GLN61 4.4 15.1 1.0 N A:ARG41 4.5 22.7 1.0 O A:GLN61 4.7 20.3 1.0 O A:PRO39 4.7 23.0 1.0 CA A:GLN61 4.7 16.3 1.0 C A:TYR59 4.7 14.0 1.0 CD1 A:ILE62 4.8 16.7 1.0 OE1 A:GLN61 4.8 50.5 1.0 C A:GLN61 4.8 16.0 1.0 CA A:GLY40 4.8 23.6 1.0 O A:HOH619 4.8 27.7 0.5

A.Wong-Sam, Y.F.Wang, Y.Zhang, A.K.Ghosh, R.W.Harrison, I.T.Weber. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of Hiv-1 Protease. Acs Omega V. 3 12132 2018.
ISSN: ESSN 2470-1343
PubMed: 30288468
DOI: 10.1021/ACSOMEGA.8B01683