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Sodium in PDB 8fui: Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group, PDB code: 8fui was solved by Y.-F.Wang, A.E.Wong-Sam, A.K.Ghosh, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.40 / 1.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.451, 86.136, 46.113, 90, 90, 90
R / Rfree (%) 13.9 / 17.6

Other elements in 8fui:

The structure of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group (pdb code 8fui). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group, PDB code: 8fui:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8fui

Go back to Sodium Binding Sites List in 8fui
Sodium binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:19.9
occ:1.00
 O A:HOH345 2.4 18.5 1.0
O A:HOH372 2.4 21.6 1.0
O A:ASP60 2.4 15.1 1.0
O A:HOH346 2.4 28.1 1.0
O A:HOH328 2.4 18.7 1.0
O A:HOH386 2.6 25.1 1.0
C A:ASP60 3.4 14.1 1.0
N A:ASP60 3.8 13.4 1.0
CA A:ASP60 4.0 13.9 1.0
O A:HOH330 4.1 28.4 1.0
O A:ARG41 4.1 17.1 1.0
O A:HOH396 4.3 30.1 0.5
CB A:GLN61 4.4 17.9 1.0
N A:GLN61 4.4 14.1 1.0
CB A:ASP60 4.4 17.4 1.0
O A:HOH391 4.4 30.0 0.5
N A:ARG41 4.5 20.2 1.0
O A:GLN61 4.5 16.6 1.0
O A:HOH401 4.6 33.5 1.0
CD1 A:ILE62 4.7 14.1 1.0
O A:PRO39 4.7 19.5 1.0
C A:TYR59 4.7 12.0 1.0
CA A:GLN61 4.7 13.6 1.0
C A:GLN61 4.7 14.2 1.0
CA A:GLY40 4.8 19.7 1.0
OE1 A:GLN61 4.9 45.8 1.0

Sodium binding site 2 out of 2 in 8fui

Go back to Sodium Binding Sites List in 8fui
Sodium binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:27.2
occ:0.75
 O B:HOH221 2.3 21.8 1.0
O B:HOH294 2.4 28.2 0.5
O B:ASP60 2.5 16.5 1.0
O B:HOH249 2.5 35.2 1.0
O B:HOH213 2.7 28.2 1.0
O B:HOH268 3.1 23.9 0.5
C B:ASP60 3.5 14.6 1.0
N B:ASP60 3.7 14.7 1.0
CA B:ASP60 4.1 13.9 1.0
O B:ARG41 4.2 16.4 1.0
O B:HOH277 4.2 22.4 0.5
O B:PRO39 4.4 17.1 1.0
CB B:ASP60 4.4 16.2 1.0
C B:TYR59 4.6 11.8 1.0
CD1 B:ILE62 4.6 15.9 1.0
N B:GLN61 4.7 14.5 1.0
CB B:GLN61 4.8 18.2 1.0
N B:ARG41 4.8 14.1 1.0
CA B:GLY40 4.8 14.3 1.0
CA B:TYR59 4.9 12.5 1.0
O B:HOH263 4.9 26.5 0.5
C B:GLN61 5.0 14.4 1.0
O B:GLN61 5.0 20.3 1.0

Reference:

A.K.Ghosh, J.L.Mishevich, S.Kovela, R.Shaktah, A.K.Ghosh, M.Johnson, Y.F.Wang, A.Wong-Sam, J.Agniswamy, M.Amano, Y.Takamatsu, S.I.Hattori, I.T.Weber, H.Mitsuya. Exploration of Imatinib and Nilotinib-Derived Templates As the P2-Ligand For Hiv-1 Protease Inhibitors: Design, Synthesis, Protein X-Ray Structural Studies, and Biological Evaluation. Eur.J.Med.Chem. V. 255 15385 2023.
ISSN: ISSN 0223-5234
PubMed: 37150084
DOI: 10.1016/J.EJMECH.2023.115385
Page generated: Wed Oct 9 11:58:11 2024

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