Sodium in PDB 3vf5: Crystal Structure of Hiv-1 Protease Mutant I47V with Novel P1'-Ligands Grl-02031

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant I47V with Novel P1'-Ligands Grl-02031:
3.4.23.16;

The structure of Crystal Structure of Hiv-1 Protease Mutant I47V with Novel P1'-Ligands Grl-02031, PDB code: 3vf5 was solved by X.X.Yu, Y.F.Wang, Y.C.E.Chang, 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 (°)	58.203, 86.394, 45.946, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.9

The structure of Crystal Structure of Hiv-1 Protease Mutant I47V with Novel P1'-Ligands Grl-02031 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Protease Mutant I47V with Novel P1'-Ligands Grl-02031 (pdb code 3vf5). 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 Mutant I47V with Novel P1'-Ligands Grl-02031, PDB code: 3vf5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Protease Mutant I47V with Novel P1'-Ligands Grl-02031


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 I47V with Novel P1'-Ligands Grl-02031 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:20.3 occ:1.00 O A:HOH606 2.3 18.7 1.0 O A:HOH616 2.3 24.4 1.0 O A:ASP60 2.4 13.6 1.0 O A:HOH656 2.5 20.1 0.5 O A:HOH665 2.5 21.1 1.0 O A:HOH666 2.6 29.1 1.0 C A:ASP60 3.4 13.0 1.0 N A:ASP60 3.8 12.2 1.0 CA A:ASP60 4.0 13.1 1.0 O A:ARG41 4.2 16.4 1.0 O A:HOH654 4.3 32.3 1.0 CB A:ASP60 4.4 15.6 1.0 N A:ARG41 4.5 23.1 1.0 CB A:GLN61 4.5 17.9 1.0 N A:GLN61 4.5 13.4 1.0 O A:PRO39 4.6 20.4 1.0 O A:GLN61 4.7 16.5 1.0 O A:HOH652 4.7 29.3 0.5 CD1 A:ILE62 4.7 16.0 1.0 C A:TYR59 4.7 10.5 1.0 CA A:GLY40 4.8 21.6 1.0 CA A:GLN61 4.8 13.8 1.0 C A:GLN61 4.8 12.5 1.0 OE1 A:GLN61 4.9 37.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Protease Mutant I47V with Novel P1'-Ligands Grl-02031


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 I47V with Novel P1'-Ligands Grl-02031 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:27.7 occ:1.00 O B:HOH1064 2.1 28.6 1.0 O B:HOH1065 2.3 25.1 1.0 O B:ASP60 2.4 15.2 1.0 O B:HOH1090 2.6 20.4 0.5 C B:ASP60 3.4 13.1 1.0 N B:ASP60 3.5 13.6 1.0 CA B:ASP60 3.9 13.9 1.0 O B:ARG41 4.2 14.9 1.0 CB B:ASP60 4.2 15.1 1.0 O B:HOH1041 4.2 29.9 1.0 C B:TYR59 4.5 10.8 1.0 N B:GLN61 4.5 12.9 1.0 O B:PRO39 4.6 15.6 1.0 CB B:GLN61 4.6 16.1 1.0 CD1 B:ILE62 4.7 13.5 1.0 CA B:TYR59 4.8 10.6 1.0 CA B:GLN61 4.9 13.4 1.0 C B:GLN61 5.0 12.2 1.0 N B:ARG41 5.0 11.8 1.0 O B:GLN61 5.0 16.1 1.0

Y.C.Chang, X.Yu, Y.Zhang, Y.Tie, Y.F.Wang, S.Yashchuk, A.K.Ghosh, R.W.Harrison, I.T.Weber. Potent Antiviral Hiv-1 Protease Inhibitor Grl-02031 Adapts to the Structures of Drug Resistant Mutants with Its P1'-Pyrrolidinone Ring. J.Med.Chem. V. 55 3387 2012.
ISSN: ISSN 0022-2623
PubMed: 22401672
DOI: 10.1021/JM300072D