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Sodium in PDB 2qd6: Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065

Enzymatic activity of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065

All present enzymatic activity of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065, PDB code: 2qd6 was solved by Y.F.Wang, Y.Tie, P.I.Boross, J.Tozser, A.K.Ghosh, R.W.Harrison, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.28
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.294, 86.228, 46.006, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20.2

Other elements in 2qd6:

The structure of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065 (pdb code 2qd6). 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 I50V with Potent Antiviral Inhibitor Grl-98065, PDB code: 2qd6:

Sodium binding site 1 out of 1 in 2qd6

Go back to Sodium Binding Sites List in 2qd6
Sodium binding site 1 out of 1 in the Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065


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 I50V with Potent Antiviral Inhibitor Grl-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:26.2
occ:1.00
 O A:HOH533 2.2 22.8 1.0
O A:ASP60 2.3 14.9 1.0
O A:HOH512 2.3 22.3 1.0
O A:HOH521 2.3 27.6 1.0
O A:HOH549 2.5 29.4 1.0
O A:HOH530 2.8 32.2 1.0
C A:ASP60 3.4 13.7 1.0
N A:ASP60 3.7 13.2 1.0
CA A:ASP60 4.0 14.1 1.0
O A:ARG41 4.2 17.6 1.0
CB A:ASP60 4.4 16.4 1.0
CB A:GLN61 4.4 18.0 1.0
N A:GLN61 4.4 14.0 1.0
N A:ARG41 4.5 22.1 1.0
O A:PRO39 4.6 24.0 1.0
O A:GLN61 4.6 18.8 1.0
C A:TYR59 4.7 10.8 1.0
CD1 A:ILE62 4.7 17.0 1.0
CA A:GLY40 4.7 22.5 1.0
CA A:GLN61 4.8 14.5 1.0
C A:GLN61 4.8 14.4 1.0
OE1 A:GLN61 4.8 42.8 1.0

Reference:

Y.F.Wang, Y.Tie, P.I.Boross, J.Tozser, A.K.Ghosh, R.W.Harrison, I.T.Weber. Potent New Antiviral Compound Shows Similar Inhibition and Structural Interactions with Drug Resistant Mutants and Wild Type Hiv-1 Protease. J.Med.Chem. V. 50 4509 2007.
ISSN: ISSN 0022-2623
PubMed: 17696515
DOI: 10.1021/JM070482Q
Page generated: Mon Oct 7 03:49:29 2024

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