Sodium in PDB 2nnk: Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir

All present enzymatic activity of Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir:
3.4.23.16;

The structure of Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir, PDB code: 2nnk was solved by Y.Tie, A.Y.Kovalevsky, P.Boross, Y.F.Wang, A.K.Ghosh, J.Tozser, R.W.Harrison, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.587, 86.003, 45.829, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 18.7

The structure of Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir (pdb code 2nnk). 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 Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir, PDB code: 2nnk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:25.3 occ:1.00 O A:HOH1127 2.2 23.1 1.0 O A:ASP60 2.4 17.3 1.0 O A:HOH1060 2.4 24.1 1.0 O A:HOH1132 2.4 36.4 1.0 O A:HOH1068 2.5 26.7 1.0 O A:HOH1064 2.8 36.3 1.0 C A:ASP60 3.4 14.7 1.0 N A:ASP60 3.8 14.6 1.0 CA A:ASP60 4.0 15.3 1.0 O A:ARG41 4.1 20.4 1.0 N A:GLN61 4.4 15.2 1.0 CB A:GLN61 4.4 19.5 1.0 CB A:ASP60 4.4 17.8 1.0 N A:ARG41 4.7 26.3 1.0 O A:PRO39 4.7 24.2 1.0 C A:TYR59 4.7 12.1 1.0 O A:GLN61 4.7 19.9 1.0 CA A:GLN61 4.7 16.1 1.0 CA A:GLY40 4.8 26.5 1.0 C A:GLN61 4.8 16.4 1.0 CD1 A:ILE62 4.8 17.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of Hiv-1 Protease Mutant I84V with A Inhibitor Saquinavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:36.9 occ:1.00 O B:HOH1112 2.1 26.8 1.0 O B:ASP160 2.4 16.1 1.0 O B:HOH1190 2.4 21.9 0.2 O B:HOH1135 2.5 38.5 1.0 O B:HOH1080 3.0 32.3 1.0 C B:ASP160 3.4 14.6 1.0 N B:ASP160 3.7 15.1 1.0 CA B:ASP160 4.0 14.2 1.0 O B:HOH1082 4.2 34.9 1.0 O B:ARG141 4.2 16.1 1.0 CB B:ASP160 4.3 17.2 1.0 O B:PRO139 4.4 20.1 1.0 N B:GLN161 4.6 14.3 1.0 C B:TYR159 4.6 12.3 1.0 CB B:GLN161 4.7 15.8 1.0 CD1 B:ILE162 4.7 17.2 1.0 O B:GLN161 4.9 18.3 1.0 CA B:TYR159 4.9 11.7 1.0 CA B:GLY140 4.9 17.1 1.0 C B:GLN161 4.9 14.0 1.0 CA B:GLN161 4.9 13.4 1.0

Y.Tie, A.Y.Kovalevsky, P.Boross, Y.F.Wang, A.K.Ghosh, J.Tozser, R.W.Harrison, I.T.Weber. Atomic Resolution Crystal Structures of Hiv-1 Protease and Mutants V82A and I84V with Saquinavir. Proteins V. 67 232 2007.
ISSN: ISSN 0887-3585
PubMed: 17243183
DOI: 10.1002/PROT.21304