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Sodium in PDB 2qd8: Hiv-1 Protease Mutant I84V with Potent Antiviral Inhibitor Grl-98065

Enzymatic activity of Hiv-1 Protease Mutant I84V with Potent Antiviral Inhibitor Grl-98065

All present enzymatic activity of Hiv-1 Protease Mutant I84V with Potent Antiviral Inhibitor Grl-98065:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Mutant I84V with Potent Antiviral Inhibitor Grl-98065, PDB code: 2qd8 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 / 1.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.423, 86.182, 45.986, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 17.5

Other elements in 2qd8:

The structure of Hiv-1 Protease Mutant I84V 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 I84V with Potent Antiviral Inhibitor Grl-98065 (pdb code 2qd8). 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 I84V with Potent Antiviral Inhibitor Grl-98065, PDB code: 2qd8:

Sodium binding site 1 out of 1 in 2qd8

Go back to Sodium Binding Sites List in 2qd8
Sodium binding site 1 out of 1 in the Hiv-1 Protease Mutant I84V 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 I84V with Potent Antiviral Inhibitor Grl-98065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:25.4
occ:1.00
 O A:HOH513 2.3 23.8 1.0
O A:HOH511 2.4 22.8 1.0
O A:ASP60 2.4 16.1 1.0
O A:HOH530 2.4 26.7 1.0
O A:HOH550 2.4 31.7 1.0
O A:HOH529 2.7 29.5 1.0
NH1 A:ARG41 3.4 29.8 0.3
C A:ASP60 3.4 15.3 1.0
N A:ASP60 3.7 13.0 1.0
CA A:ASP60 4.0 14.2 1.0
O A:ARG41 4.2 18.8 1.0
CB A:ASP60 4.4 15.4 1.0
N A:GLN61 4.4 14.8 1.0
CB A:GLN61 4.5 19.1 1.0
CZ A:ARG41 4.5 30.9 0.3
N A:ARG41 4.5 22.9 1.0
O A:HOH593 4.6 37.2 0.7
O A:GLN61 4.6 18.3 1.0
O A:PRO39 4.6 21.8 1.0
CD1 A:ILE62 4.7 14.1 1.0
C A:TYR59 4.7 10.9 1.0
CG A:ARG41 4.7 27.4 0.3
CA A:GLY40 4.8 23.5 1.0
CA A:GLN61 4.8 15.8 1.0
C A:GLN61 4.8 14.9 1.0
NH2 A:ARG41 5.0 25.5 0.3

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 04:01:20 2024

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