Sodium in PDB 4z50: Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap

The structure of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap, PDB code: 4z50 was solved by J.Agniswamy, C.-H.Shen, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.92 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.148, 48.569, 69.680, 90.00, 99.15, 90.00
R / Rfree (%)	13.8 / 19.1

The structure of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Sodium atom in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap (pdb code 4z50). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap, PDB code: 4z50:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap


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 Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:23.0 occ:0.50 O B:HOH363 2.2 27.1 1.0 O B:HOH386 2.2 32.5 0.5 O B:HOH305 2.3 48.2 1.0 O B:ASP160 2.4 13.0 1.0 O B:HOH349 2.5 31.3 1.0 O B:HOH306 2.6 26.7 1.0 C B:ASP160 3.5 11.1 1.0 O B:HOH373 3.7 45.4 1.0 N B:ASP160 3.8 11.5 1.0 O B:ARG141 3.9 17.0 1.0 OE1 B:GLN161 4.0 28.9 1.0 O B:HOH403 4.1 42.3 1.0 CA B:ASP160 4.1 11.5 1.0 N B:ARG141 4.3 16.2 1.0 O B:HOH391 4.4 25.5 1.0 CB B:GLN161 4.5 14.6 1.0 CB B:ASP160 4.6 13.6 1.0 N B:GLN161 4.6 12.2 1.0 CA B:GLY140 4.7 14.6 1.0 C B:TYR159 4.8 9.2 1.0 C B:GLN161 4.9 11.9 1.0 CA B:GLN161 4.9 12.4 1.0 O B:GLN161 4.9 14.4 1.0 C B:ARG141 4.9 14.8 1.0 C B:GLY140 5.0 14.4 1.0 CD B:GLN161 5.0 24.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap


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 Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:33.6 occ:0.50 O B:LEU119 2.7 13.6 1.0 O B:HOH336 3.4 46.2 1.0 C B:LEU119 3.8 10.7 1.0 NZ B:LYS120 4.1 23.5 1.0 CD B:LYS120 4.2 15.1 1.0 N B:LEU119 4.2 12.8 1.0 CE B:LYS120 4.2 17.9 1.0 CA B:LEU119 4.4 13.1 1.0 CB B:LEU119 4.5 14.8 1.0 N B:LYS120 4.9 9.7 1.0 CG B:LYS120 5.0 11.9 1.0 C B:GLN118 5.0 13.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:24.6 occ:0.50 O C:HOH255 2.1 24.3 0.5 O C:HOH218 2.3 28.1 1.0 O C:ASP60 2.4 16.7 1.0 O C:HOH265 2.6 31.5 0.5 O C:HOH243 2.6 28.2 0.5 C C:ASP60 3.4 16.3 1.0 N C:ASP60 3.7 13.7 1.0 O C:ARG41 4.0 19.1 1.0 CA C:ASP60 4.0 14.0 1.0 CB C:ASP60 4.3 16.6 1.0 N C:ARG41 4.5 18.6 1.0 N C:GLN61 4.6 15.3 1.0 C C:TYR59 4.7 10.0 1.0 CB C:GLN61 4.7 18.5 1.0 CA C:GLY40 4.9 17.2 1.0 O C:GLN61 4.9 18.9 1.0 C C:GLN61 4.9 15.5 1.0 CA C:GLN61 5.0 17.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Multidrug Resistant Hiv-1 Protease Clinical Isolate PR20D25N with Tucked Flap within 5.0Å range: probe atom residue distance (Å) B Occ D:Na203 b:24.6 occ:0.50 O D:HOH390 1.9 46.2 1.0 O D:HOH364 2.1 25.9 1.0 O D:HOH302 2.3 43.9 1.0 O D:HOH349 2.4 33.1 1.0 O D:ASP160 2.5 16.9 1.0 O D:HOH380 2.5 43.2 1.0 O D:HOH324 2.7 28.2 1.0 C D:ASP160 3.6 15.6 1.0 N D:ASP160 3.8 12.8 1.0 O D:ARG141 3.8 19.5 1.0 CA D:ASP160 4.2 13.6 1.0 OE1 D:GLN161 4.2 39.2 1.0 N D:ARG141 4.4 20.4 1.0 O D:HOH396 4.5 34.2 1.0 CB D:ASP160 4.5 16.0 1.0 CB D:GLN161 4.6 19.0 1.0 N D:GLN161 4.6 15.8 1.0 C D:TYR159 4.8 11.6 1.0 C D:GLN161 4.8 16.1 1.0 O D:GLN161 4.8 19.4 1.0 CA D:GLN161 4.9 15.9 1.0 C D:ARG141 4.9 18.8 1.0 CA D:GLY140 4.9 18.5 1.0

C.H.Shen, Y.C.Chang, J.Agniswamy, R.W.Harrison, I.T.Weber. Conformational Variation of An Extreme Drug Resistant Mutant of Hiv Protease. J.Mol.Graph.Model. V. 62 87 2015.
ISSN: ISSN 1093-3263
PubMed: 26397743
DOI: 10.1016/J.JMGM.2015.09.006