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Sodium in PDB 3bvb: Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir

Enzymatic activity of Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir

All present enzymatic activity of Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir:
3.4.23.16;

Protein crystallography data

The structure of Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir, PDB code: 3bvb was solved by F.Liu, 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 (°) 58.260, 85.910, 46.051, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 21

Other elements in 3bvb:

The structure of Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir (pdb code 3bvb). 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 Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir, PDB code: 3bvb:

Sodium binding site 1 out of 1 in 3bvb

Go back to Sodium Binding Sites List in 3bvb
Sodium binding site 1 out of 1 in the Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cystal Structure of Hiv-1 Active Site Mutant D25N and Inhibitor Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:28.6
occ:1.00
 O A:HOH1133 2.2 27.6 1.0
O A:HOH1087 2.3 32.6 1.0
O A:ASP60 2.4 20.8 1.0
O A:HOH1107 2.5 24.5 0.5
O A:HOH1033 2.5 30.1 1.0
O A:HOH1085 3.1 41.3 1.0
C A:ASP60 3.4 19.4 1.0
N A:ASP60 3.8 17.5 1.0
CA A:ASP60 4.0 20.9 1.0
O A:ARG41 4.2 21.7 1.0
O A:HOH1177 4.2 36.3 0.5
CB A:ASP60 4.4 24.2 1.0
N A:GLN61 4.4 18.7 1.0
CB A:GLN61 4.5 24.4 1.0
N A:ARG41 4.6 25.9 1.0
O A:PRO39 4.6 25.1 1.0
O A:GLN61 4.6 23.8 1.0
CD1 A:ILE62 4.7 21.6 1.0
C A:TYR59 4.7 16.4 1.0
C A:GLN61 4.8 18.9 1.0
CA A:GLN61 4.8 19.1 1.0
CA A:GLY40 4.8 27.6 1.0
OE1 A:GLN61 4.9 49.2 1.0

Reference:

J.M.Sayer, F.Liu, R.Ishima, I.T.Weber, J.M.Louis. Effect of the Active Site D25N Mutation on the Structure, Stability, and Ligand Binding of the Mature Hiv-1 Protease. J.Biol.Chem. V. 283 13459 2008.
ISSN: ISSN 0021-9258
PubMed: 18281688
DOI: 10.1074/JBC.M708506200
Page generated: Sun Aug 17 12:52:59 2025

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