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Sodium in PDB 3jw2: Hiv-1 Protease Mutant G86S with Darunavir

Enzymatic activity of Hiv-1 Protease Mutant G86S with Darunavir

All present enzymatic activity of Hiv-1 Protease Mutant G86S with Darunavir:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Mutant G86S with Darunavir, PDB code: 3jw2 was solved by Y.Tie, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.355, 86.145, 46.369, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 28.2

Other elements in 3jw2:

The structure of Hiv-1 Protease Mutant G86S with Darunavir also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Protease Mutant G86S with Darunavir (pdb code 3jw2). 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 Hiv-1 Protease Mutant G86S with Darunavir, PDB code: 3jw2:

Sodium binding site 1 out of 1 in 3jw2

Go back to Sodium Binding Sites List in 3jw2
Sodium binding site 1 out of 1 in the Hiv-1 Protease Mutant G86S with Darunavir


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Protease Mutant G86S with Darunavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:27.8
occ:1.00
O A:HOH1086 2.6 20.1 1.0
O A:ASP60 2.6 20.5 1.0
O A:HOH1107 2.7 38.2 1.0
O A:HOH1101 2.7 30.1 1.0
O A:HOH1072 2.7 31.8 1.0
O A:HOH1074 2.9 33.6 1.0
C A:ASP60 3.6 20.1 1.0
N A:ASP60 3.9 17.4 1.0
CA A:ASP60 4.2 19.8 1.0
O A:ARG41 4.2 24.4 0.8
O A:ARG41 4.2 24.3 0.2
CB A:GLN61 4.4 23.1 1.0
N A:ARG41 4.5 27.0 0.2
N A:ARG41 4.5 25.2 0.8
CB A:ASP60 4.5 20.9 1.0
N A:GLN61 4.6 20.1 1.0
OE1 A:GLN61 4.6 36.2 1.0
CA A:GLY40 4.7 25.5 1.0
O A:GLN61 4.7 21.0 1.0
O A:PRO39 4.7 24.2 1.0
CA A:GLN61 4.9 21.0 1.0
C A:TYR59 4.9 15.9 1.0
CD1 A:ILE62 4.9 15.9 1.0
C A:GLN61 4.9 20.5 1.0
C A:GLY40 5.0 25.8 1.0

Reference:

R.Ishima, Q.Gong, Y.Tie, I.T.Weber, J.M.Louis. Highly Conserved Glycine 86 and Arginine 87 Residues Contribute Differently to the Structure and Activity of the Mature Hiv-1 Protease Proteins V. 78 1015 2009.
ISSN: ISSN 0887-3585
PubMed: 19899162
DOI: 10.1002/PROT.22625
Page generated: Tue Dec 15 06:15:46 2020

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