Sodium in PDB 2r5p: Crystal Structure Analysis of Hiv-1 Subtype C Protease Complexed with Indinavir

The structure of Crystal Structure Analysis of Hiv-1 Subtype C Protease Complexed with Indinavir, PDB code: 2r5p was solved by R.M.Coman, A.H.Robbins, R.Mckenna, B.M.Dunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.03 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.727, 59.526, 87.384, 90.00, 95.56, 90.00
R / Rfree (%)	21.2 / 23.8

The structure of Crystal Structure Analysis of Hiv-1 Subtype C Protease Complexed with Indinavir also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure Analysis of Hiv-1 Subtype C Protease Complexed with Indinavir (pdb code 2r5p). 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 Analysis of Hiv-1 Subtype C Protease Complexed with Indinavir, PDB code: 2r5p:

Sodium binding site 1 out of 1 in the Crystal Structure Analysis of Hiv-1 Subtype C Protease Complexed with Indinavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of Hiv-1 Subtype C Protease Complexed with Indinavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Na552 b:44.0 occ:1.00 O B:THR26 2.6 19.1 1.0 O B:HOH402 2.7 40.4 1.0 NE B:ARG87 2.8 16.8 1.0 CD B:ARG87 3.4 17.0 1.0 CD A:PRO9 3.4 24.8 1.0 CG A:ARG8 3.5 25.5 1.0 C B:GLY27 3.5 18.5 1.0 CA B:GLY27 3.6 16.4 1.0 C B:THR26 3.7 18.4 1.0 CD1 A:LEU23 3.7 27.8 1.0 CA A:ARG8 3.7 26.8 1.0 O B:GLY27 3.7 17.6 1.0 OD1 B:ASP29 3.8 14.7 1.0 CB A:ARG8 3.8 27.0 1.0 CZ B:ARG87 3.8 17.6 1.0 N B:ALA28 4.0 17.6 1.0 NH2 B:ARG87 4.1 15.6 1.0 CD2 A:LEU23 4.1 29.1 1.0 N B:GLY27 4.2 17.1 1.0 CG B:ARG87 4.2 17.1 1.0 C B:ALA28 4.3 15.0 1.0 CD A:ARG8 4.3 22.3 1.0 O B:ALA28 4.3 14.3 1.0 CG A:LEU23 4.4 27.2 1.0 CG A:PRO9 4.4 25.3 1.0 N A:PRO9 4.4 25.8 1.0 N B:ASP29 4.5 15.8 1.0 C A:ARG8 4.6 26.7 1.0 CA B:ALA28 4.7 16.1 1.0 NE A:ARG8 4.7 23.3 1.0 N A:ARG8 4.7 27.1 1.0 CG B:ASP29 4.9 17.1 1.0 CA B:ASP29 4.9 17.5 1.0

R.M.Coman, A.H.Robbins, M.A.Fernandez, C.T.Gilliland, A.A.Sochet, M.M.Goodenow, R.Mckenna, B.M.Dunn. The Contribution of Naturally Occurring Polymorphisms in Altering the Biochemical and Structural Characteristics of Hiv-1 Subtype C Protease Biochemistry V. 47 731 2008.
ISSN: ISSN 0006-2960
PubMed: 18092815
DOI: 10.1021/BI7018332