Sodium in PDB 3ndt: Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure

All present enzymatic activity of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure:
3.4.23.16;

The structure of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure, PDB code: 3ndt was solved by S.Geremia, F.M.Olajuyigbe, N.Demitri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	5.00 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.294, 62.785, 59.171, 90.00, 98.32, 90.00
R / Rfree (%)	14 / 22.9

The structure of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure (pdb code 3ndt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure, PDB code: 3ndt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:65.5 occ:1.00 CA B:GLY69 3.9 28.0 1.0 OE2 B:GLU66 4.6 64.9 1.0 O B:GLY69 4.8 35.7 1.0 N B:GLY69 4.8 25.6 1.0 C B:GLY69 4.8 30.0 1.0 CD B:GLU66 5.0 48.0 1.0

Sodium binding site 2 out of 2 in the Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Protease Saquinavir:Ritonavir 1:1 Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Na100 b:64.9 occ:1.00 N C:GLY68 3.3 34.4 1.0 CG C:GLU65 3.4 48.3 1.0 O C:THR12 3.7 24.5 1.0 CB C:GLU65 3.8 35.2 1.0 O C:GLU65 3.8 23.8 1.0 N C:ALA67 3.9 28.5 1.0 C C:GLU65 3.9 29.4 1.0 CA C:GLY68 4.0 40.8 1.0 CD C:GLU65 4.1 56.5 1.0 N C:ILE66 4.2 27.2 1.0 N C:LYS14 4.2 22.0 1.0 C C:ALA67 4.3 35.7 1.0 OE1 C:GLU65 4.3 65.4 1.0 CA C:ALA67 4.4 34.5 1.0 C C:ILE66 4.4 30.7 1.0 CB C:LYS14 4.4 27.3 1.0 C C:ILE13 4.4 23.8 1.0 CA C:ILE13 4.4 21.6 1.0 C C:THR12 4.4 26.9 1.0 CA C:GLU65 4.4 27.0 1.0 CA C:ILE66 4.5 30.1 1.0 CG2 C:THR12 4.8 31.6 1.0 N C:ILE13 4.8 22.9 1.0 OE2 C:GLU65 4.9 66.4 1.0 C C:GLY68 5.0 37.5 1.0 CA C:LYS14 5.0 22.4 1.0

F.M.Olajuyigbe, N.Demitri, S.Geremia. Investigation of 2-Fold Disorder of Inhibitors and Relative Potency By Crystallizations of Hiv-1 Protease in Ritonavir and Saquinavir Mixtures Cryst.Growth Des. V. 11 4378 2011.
ISSN: ISSN 1528-7483
DOI: 10.1021/CG200514Z