Sodium in PDB 4hdp: Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519:
3.4.23.16;

The structure of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519, PDB code: 4hdp was solved by C.H.Shen, H.Zhang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.22
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.592, 85.945, 46.070, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.3

The structure of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 (pdb code 4hdp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519, PDB code: 4hdp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:18.1 occ:1.00 O B:HOH1019 2.3 16.7 1.0 O B:HOH1017 2.4 20.5 1.0 O B:HOH1018 2.4 17.4 1.0 O B:HOH1064 2.4 25.1 1.0 O B:ASP60 2.4 12.0 1.0 O B:HOH1021 2.6 23.3 1.0 C B:ASP60 3.4 11.1 1.0 N B:ASP60 3.8 10.2 1.0 O B:HOH1081 4.0 30.0 1.0 CA B:ASP60 4.1 11.8 1.0 O B:ARG41 4.1 15.9 1.0 O B:HOH1020 4.3 40.5 1.0 O B:HOH1072 4.3 44.6 1.0 CB B:GLN61 4.4 15.7 1.0 N B:ARG41 4.4 20.5 1.0 CB B:ASP60 4.4 13.2 1.0 N B:GLN61 4.5 12.5 1.0 O B:GLN61 4.6 15.1 1.0 CD1 B:ILE62 4.7 13.7 1.0 O B:PRO39 4.7 17.8 1.0 C B:TYR59 4.7 9.8 1.0 C B:GLN61 4.8 12.4 1.0 CA B:GLN61 4.8 12.7 1.0 OE1 B:GLN61 4.9 43.2 1.0 CA B:GLY40 4.9 19.7 1.0 C B:ARG41 5.0 16.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:29.4 occ:0.50 O A:HOH246 1.9 29.1 1.0 O A:HOH231 2.4 34.1 1.0 O A:HOH266 2.4 27.6 1.0 O A:ASP60 2.6 14.3 1.0 C A:ASP60 3.6 11.9 1.0 N A:ASP60 3.7 12.0 1.0 O A:HOH265 3.7 33.5 1.0 CA A:ASP60 4.1 11.9 1.0 O A:ARG41 4.1 16.0 1.0 O A:PRO39 4.3 15.4 1.0 CB A:ASP60 4.4 14.0 1.0 CD1 A:ILE62 4.6 13.2 1.0 C A:TYR59 4.6 10.0 1.0 CA A:GLY40 4.7 14.1 1.0 N A:ARG41 4.8 12.4 1.0 N A:GLN61 4.8 11.7 1.0 CA A:TYR59 4.9 9.6 1.0

H.Zhang, Y.F.Wang, C.H.Shen, J.Agniswamy, K.V.Rao, C.X.Xu, A.K.Ghosh, R.W.Harrison, I.T.Weber. Novel P2 Tris-Tetrahydrofuran Group in Antiviral Compound 1 (Grl-0519) Fills the S2 Binding Pocket of Selected Mutants of Hiv-1 Protease. J.Med.Chem. V. 56 1074 2013.
ISSN: ISSN 0022-2623
PubMed: 23298236
DOI: 10.1021/JM301519Z