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Sodium in PDB 5bry: Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate):
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate), PDB code: 5bry was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.841, 86.325, 45.630, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.5

Other elements in 5bry:

The structure of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) (pdb code 5bry). 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-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate), PDB code: 5bry:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5bry

Go back to Sodium Binding Sites List in 5bry
Sodium binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)


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-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:24.1
occ:1.00
 O A:HOH625 2.3 23.9 1.0
O A:HOH616 2.3 23.2 1.0
O A:HOH633 2.4 25.6 1.0
O A:ASP60 2.4 18.6 1.0
O A:HOH614 2.4 32.8 1.0
O A:HOH646 2.7 31.0 1.0
C A:ASP60 3.4 15.6 1.0
N A:ASP60 3.8 15.8 1.0
CA A:ASP60 4.1 16.2 1.0
O A:ARG41 4.2 21.2 1.0
CB A:ASP60 4.4 18.2 1.0
N A:GLN61 4.5 17.1 1.0
CB A:GLN61 4.5 20.5 1.0
N A:ARG41 4.5 26.1 1.0
O A:GLN61 4.6 21.9 1.0
O A:PRO39 4.7 26.4 1.0
C A:TYR59 4.7 14.4 1.0
CD1 A:ILE62 4.7 21.1 1.0
CA A:GLY40 4.8 28.5 1.0
NE2 A:GLN61 4.8 52.3 1.0
CA A:GLN61 4.8 16.8 1.0
C A:GLN61 4.8 17.6 1.0

Sodium binding site 2 out of 2 in 5bry

Go back to Sodium Binding Sites List in 5bry
Sodium binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)


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-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:23.3
occ:0.50
 O B:HOH1032 2.3 26.5 1.0
O B:HOH1046 2.5 36.1 1.0
O B:ASP60 2.5 19.4 1.0
O B:HOH1027 2.5 33.3 1.0
C B:ASP60 3.5 15.9 1.0
N B:ASP60 3.7 16.4 1.0
O B:HOH1061 3.8 36.4 1.0
CA B:ASP60 4.1 17.0 1.0
O B:ARG41 4.3 18.4 1.0
CB B:ASP60 4.3 19.1 1.0
N B:GLN61 4.6 15.6 1.0
C B:TYR59 4.6 15.1 1.0
O B:PRO39 4.7 21.4 1.0
CB B:GLN61 4.7 18.6 1.0
CD1 B:ILE62 4.7 20.1 1.0
N B:ARG41 4.9 17.3 1.0
O B:GLN61 4.9 22.1 1.0
C B:GLN61 4.9 15.4 1.0
CA B:GLY40 5.0 18.0 1.0
CA B:GLN61 5.0 16.0 1.0

Reference:

A.K.Ghosh, C.D.Martyr, H.L.Osswald, V.R.Sheri, L.A.Kassekert, S.Chen, J.Agniswamy, Y.F.Wang, H.Hayashi, M.Aoki, I.T.Weber, H.Mitsuya. Design of Hiv-1 Protease Inhibitors with Amino-Bis-Tetrahydrofuran Derivatives As P2-Ligands to Enhance Backbone-Binding Interactions: Synthesis, Biological Evaluation, and Protein-Ligand X-Ray Studies. J.Med.Chem. V. 58 6994 2015.
ISSN: ISSN 0022-2623
PubMed: 26306007
DOI: 10.1021/ACS.JMEDCHEM.5B00900
Page generated: Tue Dec 15 10:29:48 2020

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