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Sodium in PDB 4zls: Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand)

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand):
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand), PDB code: 4zls 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 / 1.53
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.740, 86.238, 46.067, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.1

Other elements in 4zls:

The structure of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) 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-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) (pdb code 4zls). 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 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand), PDB code: 4zls:

Sodium binding site 1 out of 1 in 4zls

Go back to Sodium Binding Sites List in 4zls
Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand)


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-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:23.6
occ:1.00
 O A:HOH626 2.2 22.9 1.0
O A:HOH634 2.3 27.6 1.0
O A:ASP60 2.4 17.6 1.0
O A:HOH620 2.5 26.4 1.0
O A:HOH654 2.6 33.2 1.0
O A:HOH640 2.8 30.1 1.0
C A:ASP60 3.5 16.2 1.0
N A:ASP60 3.8 17.1 1.0
CA A:ASP60 4.1 12.5 1.0
O A:ARG41 4.2 19.4 1.0
O A:PRO39 4.5 24.3 1.0
CB A:GLN61 4.5 21.9 1.0
N A:GLN61 4.5 14.4 1.0
O A:GLN61 4.5 18.7 1.0
CB A:ASP60 4.5 18.1 1.0
N A:ARG41 4.6 24.4 1.0
CD1 A:ILE62 4.7 21.0 1.0
CA A:GLY40 4.7 22.8 1.0
C A:TYR59 4.7 17.5 1.0
C A:GLN61 4.7 20.6 1.0
CA A:GLN61 4.8 20.1 1.0
C A:GLY40 5.0 22.0 1.0

Reference:

A.K.Ghosh, X.Yu, H.L.Osswald, J.Agniswamy, Y.F.Wang, M.Amano, I.T.Weber, H.Mitsuya. Structure-Based Design of Potent Hiv-1 Protease Inhibitors with Modified P1-Biphenyl Ligands: Synthesis, Biological Evaluation, and Enzyme-Inhibitor X-Ray Structural Studies. J.Med.Chem. V. 58 5334 2015.
ISSN: ISSN 0022-2623
PubMed: 26107245
DOI: 10.1021/ACS.JMEDCHEM.5B00676
Page generated: Mon Oct 7 19:44:02 2024

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