Atomistry » Sodium » PDB 4tmw-4u9k » 4u8w
Atomistry »
  Sodium »
    PDB 4tmw-4u9k »
      4u8w »

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: Sun Aug 17 21:52:03 2025

Last articles

Na in 8C6G
Na in 8C6O
Na in 8C61
Na in 8C4D
Na in 8C59
Na in 8C4N
Na in 8C56
Na in 8BYK
Na in 8C0G
Na in 8C25
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy