Sodium in PDB 5jfp: Hiv-1 Wild Type Protease with Grl-097-13A (A Adamantane P1-Ligand with Bis-Thf in P2 and Isobutylamine in P1')

The structure of Hiv-1 Wild Type Protease with Grl-097-13A (A Adamantane P1-Ligand with Bis-Thf in P2 and Isobutylamine in P1'), PDB code: 5jfp was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.100, 86.140, 45.949, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.7

The structure of Hiv-1 Wild Type Protease with Grl-097-13A (A Adamantane P1-Ligand with Bis-Thf in P2 and Isobutylamine in P1') also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-097-13A (A Adamantane P1-Ligand with Bis-Thf in P2 and Isobutylamine in P1') (pdb code 5jfp). 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 Hiv-1 Wild Type Protease with Grl-097-13A (A Adamantane P1-Ligand with Bis-Thf in P2 and Isobutylamine in P1'), PDB code: 5jfp:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-097-13A (A Adamantane P1-Ligand with Bis-Thf in P2 and Isobutylamine in P1')


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Wild Type Protease with Grl-097-13A (A Adamantane P1-Ligand with Bis-Thf in P2 and Isobutylamine in P1') within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:20.1 occ:1.00 O A:HOH628 2.2 19.3 1.0 O A:HOH608 2.3 22.5 1.0 O A:ASP60 2.5 14.6 1.0 O A:HOH652 2.5 32.3 1.0 O A:HOH625 2.6 25.6 1.0 O A:HOH646 2.8 33.4 1.0 C A:ASP60 3.4 10.0 1.0 N A:ASP60 3.7 12.4 1.0 CA A:ASP60 4.0 14.0 1.0 O A:ARG41 4.1 17.3 1.0 CB A:ASP60 4.4 17.5 1.0 N A:GLN61 4.5 14.7 1.0 CB A:GLN61 4.5 20.2 1.0 N A:ARG41 4.6 18.6 1.0 O A:GLN61 4.7 20.3 1.0 O A:PRO39 4.7 19.0 1.0 CA A:GLY40 4.7 21.6 1.0 C A:TYR59 4.7 11.8 1.0 CD1 A:ILE62 4.7 17.1 1.0 C A:GLN61 4.9 14.3 1.0 CA A:GLN61 4.9 15.3 1.0 C A:GLY40 5.0 21.7 1.0

A.K.Ghosh, H.L.Osswald, K.Glauninger, J.Agniswamy, Y.F.Wang, H.Hayashi, M.Aoki, I.T.Weber, H.Mitsuya. Probing Lipophilic Adamantyl Group As the P1-Ligand For Hiv-1 Protease Inhibitors: Design, Synthesis, Protein X-Ray Structural Studies, and Biological Evaluation. J.Med.Chem. V. 59 6826 2016.
ISSN: ISSN 0022-2623
PubMed: 27389367
DOI: 10.1021/ACS.JMEDCHEM.6B00639