Sodium in PDB 6u7p: Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand

The structure of Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand, PDB code: 6u7p was solved by Y.-F.Wang, D.W.Kneller, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.69 / 1.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.491, 86.097, 46.086, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14.1

The structure of Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand (pdb code 6u7p). 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-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand, PDB code: 6u7p:

Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the 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 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:19.7 occ:1.00 O A:HOH333 2.3 19.2 1.0 O A:HOH366 2.4 23.3 1.0 O A:ASP60 2.4 14.0 1.0 O A:HOH359 2.4 20.4 0.5 O A:HOH324 2.4 20.0 1.0 O A:HOH385 2.7 26.3 1.0 C A:ASP60 3.4 13.0 1.0 N A:ASP60 3.8 12.8 1.0 CA A:ASP60 4.0 13.1 1.0 O A:HOH338 4.1 30.2 1.0 O A:ARG41 4.2 18.2 1.0 CB A:GLN61 4.4 17.2 1.0 CB A:ASP60 4.4 16.1 1.0 N A:GLN61 4.4 13.8 1.0 N A:ARG41 4.5 22.2 1.0 O A:HOH392 4.5 27.4 0.5 O A:GLN61 4.6 16.1 1.0 O A:PRO39 4.6 21.8 1.0 CD1 A:ILE62 4.7 13.6 1.0 CA A:GLN61 4.7 14.2 1.0 C A:GLN61 4.7 13.1 1.0 CA A:GLY40 4.7 21.1 1.0 C A:TYR59 4.7 11.5 1.0 OE1 A:GLN61 4.9 53.6 1.0 C A:GLY40 5.0 19.1 1.0

A.K.Ghosh, Z.Xia, S.Kovela, W.L.Robinson, M.E.Johnson, D.W.Kneller, Y.F.Wang, M.Aoki, Y.Takamatsu, I.T.Weber, H.Mitsuya. Potent Hiv-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-Ray Structural Studies. Chemmedchem V. 14 1863 2019.
ISSN: ESSN 1860-7187
PubMed: 31549492
DOI: 10.1002/CMDC.201900508