Sodium in PDB 3vf7: Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031:
3.4.23.16;

The structure of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031, PDB code: 3vf7 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 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.820, 86.242, 46.005, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.5

The structure of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 (pdb code 3vf7). 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 L76V with Novel P1'-Ligands Grl-02031, PDB code: 3vf7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Protease Mutant L76V 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 L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:35.0 occ:1.00 O A:HOH1076 2.2 21.0 0.5 O A:HOH1041 2.3 27.0 1.0 O A:HOH1063 2.4 33.8 1.0 O A:HOH1071 2.4 24.8 0.5 O A:HOH1105 2.5 25.3 0.5 O A:HOH1016 2.7 16.2 1.0 OH A:TYR59 3.8 13.8 1.0 CA A:SER37 4.2 17.4 1.0 NH2 A:ARG57 4.2 19.1 1.0 O A:LEU38 4.3 14.9 1.0 N A:LEU38 4.3 14.3 1.0 O A:HOH1025 4.3 16.6 1.0 O A:HOH1093 4.4 28.5 0.5 O A:MET36 4.5 16.6 1.0 O1 A:GOL208 4.6 18.8 0.5 CB A:SER37 4.6 27.2 1.0 O A:HOH1083 4.7 24.6 0.5 OG A:SER37 4.7 41.2 1.0 C A:SER37 4.8 16.6 1.0 CZ A:TYR59 4.9 10.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Protease Mutant L76V 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 L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:24.6 occ:1.00 O B:HOH630 2.2 18.4 1.0 O B:HOH674 2.4 27.4 0.5 O B:HOH632 2.4 27.2 1.0 O B:ASP60 2.5 15.1 1.0 O B:HOH631 2.6 22.4 1.0 O B:HOH634 2.9 27.9 1.0 C B:ASP60 3.5 14.4 1.0 N B:ASP60 3.6 13.2 1.0 CA B:ASP60 4.0 14.0 1.0 O B:ARG41 4.2 14.9 1.0 CB B:ASP60 4.4 18.8 1.0 O B:PRO39 4.4 19.5 1.0 CB B:GLN61 4.4 19.6 1.0 N B:GLN61 4.5 14.6 1.0 N B:ARG41 4.5 19.4 1.0 C B:TYR59 4.6 10.5 1.0 CD1 B:ILE62 4.7 14.2 1.0 CA B:GLY40 4.7 19.8 1.0 O B:GLN61 4.8 20.0 1.0 CA B:GLN61 4.8 15.1 1.0 C B:GLN61 4.9 14.0 1.0 C B:GLY40 5.0 17.4 1.0 CA B:TYR59 5.0 9.4 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