Sodium in PDB 2hb3: Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579

All present enzymatic activity of Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579:
3.4.23.4;

The structure of Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579, PDB code: 2hb3 was solved by A.Y.Kovalevsky, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.080, 86.480, 45.940, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 19.2

The structure of Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579 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 Potent Inhibitor GRL06579 (pdb code 2hb3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579, PDB code: 2hb3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579


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 Potent Inhibitor GRL06579 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:21.8 occ:1.00 O A:HOH1098 2.3 22.9 1.0 O A:HOH1144 2.3 31.4 1.0 O A:ASP60 2.4 14.8 1.0 O A:HOH1045 2.4 21.6 1.0 O A:HOH1041 2.4 22.1 1.0 O A:HOH1064 2.8 28.7 1.0 C A:ASP60 3.4 14.2 1.0 N A:ASP60 3.8 13.6 1.0 CA A:ASP60 4.0 14.0 1.0 O A:HOH1169 4.1 33.6 1.0 O A:ARG41 4.2 17.5 1.0 CB A:GLN61 4.4 16.7 1.0 CB A:ASP60 4.4 16.5 1.0 N A:GLN61 4.4 13.8 1.0 O A:HOH1175 4.5 39.3 1.0 O A:GLN61 4.6 18.4 1.0 N A:ARG41 4.6 21.7 1.0 O A:HOH1155 4.7 40.8 1.0 O A:PRO39 4.7 21.4 1.0 C A:TYR59 4.7 11.5 1.0 CD1 A:ILE62 4.7 15.9 1.0 CA A:GLN61 4.7 14.8 1.0 C A:GLN61 4.8 15.3 1.0 OE1 A:GLN61 4.9 50.5 1.0 CA A:GLY40 4.9 22.9 1.0

Sodium binding site 2 out of 2 in the Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wild-Type Hiv-1 Protease in Complex with Potent Inhibitor GRL06579 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na905 b:32.3 occ:1.00 O B:HOH1066 2.3 43.8 1.0 O B:HOH1044 2.3 22.2 1.0 O B:ASP60 2.4 15.6 1.0 O B:HOH1115 2.6 43.3 1.0 O B:HOH1103 2.7 32.3 1.0 C B:ASP60 3.4 14.1 1.0 N B:ASP60 3.7 14.5 1.0 CA B:ASP60 4.0 14.0 1.0 O B:HOH1085 4.2 29.4 1.0 O B:ARG41 4.3 16.2 1.0 CB B:ASP60 4.3 15.1 1.0 N B:GLN61 4.5 14.3 1.0 C B:TYR59 4.6 11.8 1.0 O B:PRO39 4.6 17.9 1.0 CB B:GLN61 4.6 16.8 1.0 CD1 B:ILE62 4.7 14.9 1.0 CA B:GLN61 4.9 13.7 1.0 O B:GLN61 4.9 18.1 1.0 C B:GLN61 4.9 13.9 1.0 N B:ARG41 4.9 13.5 1.0 CA B:TYR59 4.9 11.6 1.0

A.K.Ghosh, P.R.Sridhar, S.Leshchenko, A.K.Hussain, J.Li, A.Y.Kovalevsky, D.E.Walters, J.E.Wedekind, V.Grum-Tokars, D.Das, Y.Koh, K.Maeda, H.Gatanaga, I.T.Weber, H.Mitsuya. Structure-Based Design of Novel Hiv-1 Protease Inhibitors to Combat Drug Resistance. J.Med.Chem. V. 49 5252 2006.
ISSN: ISSN 0022-2623
PubMed: 16913714
DOI: 10.1021/JM060561M