Sodium in PDB 6u7o: Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand, PDB code: 6u7o was solved by Y.-F.Wang, D.W.Kneller, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.41 / 1.33
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.921, 86.479, 45.875, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 17.7

Other elements in 6u7o:

The structure of Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand 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-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand (pdb code 6u7o). 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-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand, PDB code: 6u7o:

Sodium binding site 1 out of 1 in 6u7o

Go back to Sodium Binding Sites List in 6u7o
Sodium binding site 1 out of 1 in the Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the 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-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:24.0
occ:1.00
O A:HOH632 2.3 22.2 1.0
O A:HOH657 2.4 28.3 0.8
O A:ASP60 2.4 18.0 1.0
O A:HOH660 2.4 24.2 1.0
O A:HOH615 2.4 22.7 1.0
O A:HOH675 2.7 29.7 1.0
C A:ASP60 3.4 15.9 1.0
N A:ASP60 3.8 16.2 1.0
CA A:ASP60 4.1 16.3 1.0
O A:ARG41 4.1 19.7 1.0
O A:HOH625 4.2 33.8 1.0
O A:HOH684 4.3 34.5 0.5
CB A:GLN61 4.4 20.1 1.0
CB A:ASP60 4.4 19.3 1.0
N A:GLN61 4.5 16.4 1.0
O A:HOH685 4.5 31.8 0.5
N A:ARG41 4.5 27.0 1.0
O A:GLN61 4.6 19.3 1.0
CD1 A:ILE62 4.6 17.1 1.0
O A:PRO39 4.7 24.8 1.0
C A:TYR59 4.7 15.2 1.0
CA A:GLY40 4.8 25.6 1.0
C A:GLN61 4.8 14.9 1.0
CA A:GLN61 4.8 16.7 1.0
C A:GLY40 5.0 22.7 1.0

Reference:

A.K.Ghosh, Z.Xia, S.Kovela, W.L.Robinson, M.E.Johnson, D.W.Kneller, Y.F.Wang, M.Aoki, Y.Takamatsu, I.T.Weber, H.Mitsuya. Potent Hiv-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-Ray Structural Studies. Chemmedchem V. 14 1863 2019.
ISSN: ESSN 1860-7187
PubMed: 31549492
DOI: 10.1002/CMDC.201900508
Page generated: Tue Dec 15 14:29:32 2020

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