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

Protein crystallography data

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

Other elements in 2r5p:

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

Sodium Binding Sites:

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 2r5p

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Tue Dec 15 05:55:46 2020

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