Sodium in PDB 3nu5: Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir:
3.4.23.16;

The structure of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir, PDB code: 3nu5 was solved by Y.-F.Wang, C.H.Shen, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.953, 86.011, 46.209, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 19.3

The structure of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir (pdb code 3nu5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir, PDB code: 3nu5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 Mutant I50V with Antiviral Drug Amprenavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:20.6 occ:1.00 O A:HOH1085 2.2 32.7 1.0 O A:HOH1013 2.4 17.7 1.0 O A:HOH1022 2.4 19.8 1.0 O A:ASP60 2.4 14.2 1.0 O A:HOH1073 2.4 26.2 1.0 O A:HOH1066 2.7 27.2 1.0 C A:ASP60 3.4 13.7 1.0 N A:ASP60 3.8 12.2 1.0 CA A:ASP60 4.0 13.6 1.0 O A:ARG41 4.2 16.2 1.0 CB A:ASP60 4.4 16.0 1.0 CB A:GLN61 4.4 17.4 1.0 N A:GLN61 4.5 13.8 1.0 N A:ARG41 4.5 18.5 1.0 O A:HOH1119 4.5 24.8 0.5 O A:GLN61 4.7 16.3 1.0 O A:PRO39 4.7 19.4 1.0 C A:TYR59 4.7 10.3 1.0 CD1 A:ILE62 4.7 14.5 1.0 CA A:GLN61 4.8 14.4 1.0 OE1 A:GLN61 4.8 40.3 1.0 C A:GLN61 4.8 14.2 1.0 CA A:GLY40 4.8 17.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


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 Mutant I50V with Antiviral Drug Amprenavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:21.8 occ:0.50 O B:HOH1023 2.3 21.4 1.0 O B:ASP160 2.4 14.7 1.0 O B:HOH1113 2.4 22.9 0.5 O B:HOH1177 3.0 17.2 0.5 C B:ASP160 3.4 12.4 1.0 N B:ASP160 3.7 14.0 1.0 CA B:ASP160 4.0 13.7 1.0 O B:HOH1046 4.1 32.2 1.0 CB B:ASP160 4.3 15.8 1.0 O B:ARG141 4.4 14.9 1.0 O B:PRO139 4.5 16.3 1.0 CD1 B:ILE162 4.5 17.8 1.0 N B:GLN161 4.5 12.7 1.0 C B:TYR159 4.6 10.2 1.0 CB B:GLN161 4.6 17.0 1.0 C B:GLN161 4.8 12.8 1.0 O B:GLN161 4.8 16.1 1.0 CA B:GLN161 4.9 12.8 1.0 CA B:GLY140 4.9 14.4 1.0 O B:HOH1147 4.9 26.8 0.5 CA B:TYR159 4.9 10.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hiv-1 Protease Mutant I50V with Antiviral Drug Amprenavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:26.0 occ:0.50 O B:HOH1158 2.0 24.3 0.5 O B:HOH1159 2.4 23.2 0.5 O B:HOH1162 2.4 22.7 0.5 O B:HOH1160 2.5 24.7 0.5 O B:HOH1161 2.5 19.3 0.2 O B:HOH1157 2.7 19.5 1.0 OH B:TYR159 3.8 16.0 1.0 CA B:SER137 4.1 19.3 0.3 CA B:SER137 4.1 19.3 0.7 OG B:SER137 4.1 30.9 0.7 OG B:SER137 4.1 21.8 0.3 O B:HOH1050 4.2 18.5 1.0 O B:LEU138 4.3 16.1 1.0 N B:LEU138 4.4 15.6 1.0 CB B:SER137 4.4 22.7 0.3 NH2 B:ARG157 4.4 25.1 1.0 CB B:SER137 4.5 23.8 0.7 O B:MET136 4.5 19.6 1.0 C B:SER137 4.8 16.4 1.0 O B:HOH1129 4.9 19.0 0.2 CZ B:TYR159 4.9 14.2 1.0

C.H.Shen, Y.F.Wang, A.Y.Kovalevsky, R.W.Harrison, I.T.Weber. Amprenavir Complexes with Hiv-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters. Febs J. V. 277 3699 2010.
ISSN: ISSN 1742-464X
PubMed: 20695887
DOI: 10.1111/J.1742-4658.2010.07771.X