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Sodium in PDB 4u8w: Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand):
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand), PDB code: 4u8w 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 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.539, 85.989, 46.210, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.8

Other elements in 4u8w:

The structure of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) (pdb code 4u8w). 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-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand), PDB code: 4u8w:

Sodium binding site 1 out of 1 in 4u8w

Go back to Sodium Binding Sites List in 4u8w
Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-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-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:24.2
occ:1.00
 O A:HOH323 2.3 26.1 1.0
O A:HOH322 2.3 20.6 1.0
O A:ASP60 2.4 14.9 1.0
O A:HOH368 2.5 31.9 1.0
O A:HOH321 2.5 19.8 1.0
O A:HOH355 2.8 35.4 1.0
C A:ASP60 3.4 14.1 1.0
N A:ASP60 3.8 12.7 1.0
O A:HOH367 4.0 24.6 0.5
CA A:ASP60 4.1 14.1 1.0
O A:ARG41 4.2 19.2 1.0
CB A:GLN61 4.4 19.2 1.0
N A:GLN61 4.5 13.9 1.0
CB A:ASP60 4.5 17.1 1.0
N A:ARG41 4.5 23.4 1.0
CD1 A:ILE62 4.6 16.3 1.0
O A:PRO39 4.6 22.8 1.0
O A:GLN61 4.6 19.0 1.0
O A:HOH347 4.7 35.6 0.5
C A:TYR59 4.7 10.6 1.0
CA A:GLY40 4.7 26.4 1.0
C A:GLN61 4.8 14.5 1.0
CA A:GLN61 4.8 14.9 1.0
OE1 A:GLN61 4.8 39.2 1.0

Reference:

A.K.Ghosh, S.Yashchuk, A.Mizuno, N.Chakraborty, J.Agniswamy, Y.F.Wang, M.Aoki, P.M.Gomez, M.Amano, I.T.Weber, H.Mitsuya. Design of Gem-Difluoro-Bis-Tetrahydrofuran As P2 Ligand For Hiv-1 Protease Inhibitors to Improve Brain Penetration: Synthesis, X-Ray Studies, and Biological Evaluation. Chemmedchem 2014.
ISSN: ESSN 1860-7187
PubMed: 25336073
DOI: 10.1002/CMDC.201402358
Page generated: Mon Oct 7 18:33:22 2024

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