Sodium in PDB 3d1y: Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Saquina

All present enzymatic activity of Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Saquina:
3.4.23.16;

The structure of Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Saquina, PDB code: 3d1y was solved by F.Liu, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.720, 85.940, 46.380, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.4

The structure of Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Saquina also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Saquina (pdb code 3d1y). 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 Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Saquina, PDB code: 3d1y:

Sodium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Mutant I54V and Inhibitor Saquina


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 Mutant I54V and Inhibitor Saquina within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:19.4 occ:1.00 O A:HOH1024 2.3 19.1 1.0 O A:ASP60 2.4 13.7 1.0 O A:HOH1045 2.4 21.9 1.0 O A:HOH1088 2.5 27.7 1.0 O A:HOH1040 2.5 19.9 1.0 O A:HOH1089 2.6 28.6 1.0 C A:ASP60 3.4 12.6 1.0 N A:ASP60 3.8 12.3 1.0 CA A:ASP60 4.0 12.8 1.0 O A:HOH1141 4.1 34.6 1.0 O A:ARG41 4.2 16.2 1.0 O A:HOH1216 4.3 46.4 1.0 CB A:ASP60 4.4 16.6 1.0 CB A:GLN61 4.4 17.2 1.0 N A:GLN61 4.4 12.4 1.0 N A:ARG41 4.5 19.9 1.0 O A:GLN61 4.6 16.8 1.0 O A:HOH1135 4.6 43.1 1.0 O A:PRO39 4.7 19.6 1.0 CD1 A:ILE62 4.7 14.2 1.0 C A:TYR59 4.7 10.8 1.0 CA A:GLN61 4.7 14.1 1.0 C A:GLN61 4.8 13.3 1.0 CA A:GLY40 4.8 20.1 1.0 NE2 A:GLN61 4.8 41.8 1.0

F.Liu, A.Y.Kovalevsky, Y.Tie, A.K.Ghosh, R.W.Harrison, I.T.Weber. Effect of Flap Mutations on Structure of Hiv-1 Protease and Inhibition By Saquinavir and Darunavir. J.Mol.Biol. V. 381 102 2008.
ISSN: ISSN 0022-2836
PubMed: 18597780
DOI: 10.1016/J.JMB.2008.05.062