Sodium in PDB 6dif: Wild-Type Hiv-1 Protease in Complex with Tipranavir

The structure of Wild-Type Hiv-1 Protease in Complex with Tipranavir, PDB code: 6dif 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)	25.00 / 1.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.300, 86.259, 46.005, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.7

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

Fluorine	(F)	6 atoms
Chlorine	(Cl)	3 atoms

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

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


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 Tipranavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:17.9 occ:1.00 O A:ASP60 2.3 12.9 1.0 O A:HOH662 2.3 21.5 1.0 O A:HOH632 2.4 15.9 1.0 O A:HOH608 2.4 31.5 1.0 O A:HOH646 2.4 17.6 1.0 O A:HOH680 2.7 27.1 1.0 C A:ASP60 3.3 12.2 1.0 N A:ASP60 3.7 10.7 1.0 O A:HOH660 4.0 32.5 1.0 CA A:ASP60 4.0 11.8 1.0 O A:ARG41 4.3 14.5 1.0 O A:HOH694 4.3 31.2 0.5 CB A:GLN61 4.4 14.6 1.0 CB A:ASP60 4.4 13.9 1.0 N A:GLN61 4.4 12.0 1.0 N A:ARG41 4.5 19.5 1.0 O A:GLN61 4.5 15.4 1.0 O A:PRO39 4.7 17.9 1.0 C A:TYR59 4.7 9.1 1.0 C A:GLN61 4.7 12.9 1.0 CA A:GLN61 4.7 12.4 1.0 CD1 A:ILE62 4.7 14.5 1.0 OE1 A:GLN61 4.8 41.9 1.0 CA A:GLY40 4.9 17.9 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