Sodium in PDB 6dj5: Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand)

The structure of Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand), PDB code: 6dj5 was solved by A.E.Wong-Sam, Y.F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.00 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.672, 86.337, 45.997, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.3

The structure of Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand) also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand) (pdb code 6dj5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand), PDB code: 6dj5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand)


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 with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:27.6 occ:1.00 O A:HOH231 2.2 33.0 1.0 O A:HOH218 2.3 25.5 1.0 O A:ASP60 2.4 15.2 1.0 O A:HOH201 2.6 27.8 1.0 O A:HOH234 3.1 19.2 0.5 C A:ASP60 3.4 18.9 1.0 N A:ASP60 3.7 12.6 1.0 CA A:ASP60 4.0 17.3 1.0 O A:ARG41 4.3 17.4 1.0 CB A:GLN61 4.4 20.4 1.0 O A:PRO39 4.4 22.1 1.0 CB A:ASP60 4.4 22.5 1.0 N A:GLN61 4.4 16.2 1.0 CA A:GLY40 4.6 21.7 1.0 N A:ARG41 4.6 19.8 1.0 C A:TYR59 4.6 17.6 1.0 O A:GLN61 4.7 25.7 1.0 CD1 A:ILE62 4.7 12.1 1.0 CA A:GLN61 4.8 12.6 1.0 C A:GLN61 4.8 20.8 1.0 C A:GLY40 4.9 22.6 1.0

Sodium binding site 2 out of 2 in the Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Protease with Mutation L76V in Complex with Grl-0519 (Tris- Tetrahydrofuran As P2 Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:48.2 occ:0.50 O B:HOH1123 2.4 37.6 1.0 O B:HOH1155 2.5 19.1 0.5 O B:ASP60 2.9 17.3 1.0 O1 B:GOL208 3.5 14.4 0.5 O B:HOH1169 3.5 35.6 0.5 O B:HOH1144 3.9 32.1 1.0 C B:ASP60 3.9 16.8 1.0 N B:ASP60 4.2 14.2 1.0 O B:PRO39 4.5 19.8 1.0 CA B:ASP60 4.6 17.2 1.0 O B:ARG41 4.6 17.1 1.0 CB B:GLN61 4.7 17.6 0.5 O2 B:GOL208 4.8 28.8 0.5 CA B:GLY40 4.8 17.4 1.0 C1 B:GOL208 4.8 9.0 0.5 O B:HOH1166 4.9 28.9 0.5 N B:GLN61 5.0 15.7 1.0 O B:GLN61 5.0 21.8 1.0

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