Fluorine in PDB 5sre: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer:
3.4.19.121;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer, PDB code: 5sre was solved by G.J.Correy, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.65 / 1.05
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.668, 88.668, 39.475, 90, 90, 90
R / Rfree (%)	13.4 / 15.2

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer (pdb code 5sre). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer, PDB code: 5sre:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:12.4 occ:0.07 F1 A:R8R201 0.0 12.4 0.1 H7 A:R8R202 0.7 14.6 0.1 O A:HOH452 1.3 15.0 0.8 C9 A:R8R201 1.4 12.7 0.1 O A:HOH550 1.4 36.0 0.9 N2 A:R8R202 1.6 12.2 0.1 C8 A:R8R201 2.4 13.0 0.1 C10 A:R8R201 2.4 12.8 0.1 HB2 A:ALA52 2.5 12.4 0.2 H5 A:R8R201 2.5 15.4 0.1 H4 A:R8R201 2.6 15.6 0.1 C7 A:R8R202 2.6 12.7 0.1 HB2 A:ALA52 2.6 14.1 0.8 C12 A:R8R202 2.6 12.2 0.1 H4 A:R8R202 2.9 16.1 0.1 C8 A:R8R202 3.1 13.4 0.1 N3 A:R8R202 3.1 12.6 0.1 CB A:ALA52 3.3 10.3 0.2 HB1 A:ALA52 3.4 12.4 0.2 O A:HOH542 3.4 31.7 0.8 O A:HOH471 3.5 45.5 0.8 CB A:ALA52 3.5 11.7 0.8 C7 A:R8R201 3.6 13.2 0.1 C11 A:R8R201 3.6 13.0 0.1 HB3 A:ALA52 3.7 12.4 0.2 HB1 A:ALA52 3.7 14.1 0.8 C6 A:R8R202 3.8 12.8 0.1 C5 A:R8R202 3.8 12.5 0.1 HB3 A:ALA52 3.9 14.1 0.8 O A:GLY48 4.0 11.3 0.8 C6 A:R8R201 4.1 13.4 0.1 H6 A:R8R201 4.4 15.6 0.1 HA A:ALA52 4.4 11.8 0.2 O A:GLY48 4.4 12.1 0.2 C13 A:R8R202 4.5 12.8 0.1 CA A:ALA52 4.5 9.8 0.2 C9 A:R8R202 4.5 14.1 0.1 HA A:ALA52 4.5 12.4 0.8 H A:ALA52 4.5 11.6 0.8 CA A:ALA52 4.5 10.4 0.8 C A:GLY48 4.7 10.6 0.8 H A:ALA52 4.7 11.6 0.2 N A:ALA52 4.8 9.7 0.8 HA2 A:GLY48 4.8 13.8 0.8 HA A:VAL49 4.9 15.7 0.2 N2 A:R8R201 4.9 13.3 0.1 N A:ALA52 4.9 9.7 0.2 C11 A:R8R202 5.0 13.5 0.1

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562530 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:15.1 occ:0.15 F1 A:R8R202 0.0 15.1 0.1 OD1 A:ASP22 1.3 21.7 0.8 C9 A:R8R202 1.4 14.1 0.1 H7 A:R8R201 1.5 16.0 0.1 HG23 A:VAL24 2.2 25.7 0.2 N2 A:R8R201 2.3 13.3 0.1 H A:VAL24 2.3 19.5 0.8 C8 A:R8R202 2.4 13.4 0.1 C10 A:R8R202 2.4 14.0 0.1 CG A:ASP22 2.4 21.8 0.8 H5 A:R8R202 2.5 16.8 0.1 H4 A:R8R202 2.6 16.1 0.1 H A:ILE23 2.6 25.8 0.2 HG23 A:VAL24 2.7 23.5 0.8 H A:VAL24 2.8 25.8 0.2 H4 A:R8R201 2.8 15.6 0.1 HG22 A:ILE23 2.9 16.9 0.8 HB A:VAL24 3.0 22.8 0.8 HG22 A:ILE23 3.0 24.9 0.2 CG2 A:VAL24 3.0 21.4 0.2 OD2 A:ASP22 3.0 23.0 0.2 OD1 A:ASP22 3.0 22.5 0.2 HG22 A:VAL24 3.0 25.7 0.2 CG A:ASP22 3.0 22.5 0.2 C7 A:R8R201 3.1 13.2 0.1 O A:HOH471 3.1 45.5 0.8 H A:ILE23 3.1 18.6 0.8 OD2 A:ASP22 3.1 23.6 0.8 HD1 A:PHE156 3.1 21.4 0.2 N A:VAL24 3.2 16.3 0.8 N A:ILE23 3.3 21.5 0.2 C8 A:R8R201 3.3 13.0 0.1 CG2 A:VAL24 3.3 19.6 0.8 N A:ILE23 3.3 15.5 0.8 HA A:ASP22 3.3 21.5 0.8 HG21 A:VAL24 3.4 25.7 0.2 HA A:ASP22 3.4 26.1 0.2 HE1 A:PHE156 3.4 21.3 0.2 C12 A:R8R201 3.4 13.7 0.1 HG21 A:VAL24 3.5 23.5 0.8 CB A:VAL24 3.5 19.0 0.8 CB A:ASP22 3.6 20.0 0.8 N A:VAL24 3.6 21.5 0.2 C A:ASP22 3.6 16.3 0.8 C7 A:R8R202 3.6 12.7 0.1 C11 A:R8R202 3.6 13.5 0.1 CA A:ASP22 3.7 17.9 0.8 CD1 A:PHE156 3.8 17.8 0.2 CG2 A:ILE23 3.8 14.1 0.8 HB1 A:ALA52 3.8 14.1 0.8 CE1 A:PHE156 3.9 17.8 0.2 CG2 A:ILE23 3.9 20.8 0.2 HG23 A:ILE23 3.9 16.9 0.8 CA A:ASP22 3.9 21.8 0.2 CA A:VAL24 3.9 17.7 0.8 N3 A:R8R201 4.0 14.0 0.1 C A:ASP22 4.0 21.6 0.2 CB A:ASP22 4.0 22.1 0.2 O A:HOH417 4.1 23.6 0.9 C A:ILE23 4.1 14.9 0.8 C6 A:R8R202 4.1 12.8 0.1 HB1 A:ALA52 4.1 12.4 0.2 H A:GLU25 4.1 23.8 0.8 HB2 A:ASP22 4.2 24.0 0.8 CA A:ILE23 4.2 14.7 0.8 CA A:ILE23 4.2 21.1 0.2 CB A:VAL24 4.2 21.4 0.2 HG22 A:VAL24 4.2 23.5 0.8 HB3 A:ASP22 4.2 24.0 0.8 HB3 A:ALA52 4.3 14.1 0.8 HG21 A:ILE23 4.3 24.9 0.2 C6 A:R8R201 4.3 13.4 0.1 C A:ILE23 4.4 21.4 0.2 HB A:VAL24 4.4 25.7 0.2 O A:HOH542 4.4 31.7 0.8 H6 A:R8R202 4.4 16.2 0.1 O A:ASP22 4.4 17.2 0.8 HB A:ILE23 4.4 24.9 0.2 H A:GLU25 4.4 25.9 0.2 CB A:ILE23 4.5 20.8 0.2 HG23 A:ILE23 4.5 24.9 0.2 CB A:ALA52 4.5 11.7 0.8 HB2 A:ASP22 4.5 26.6 0.2 HG21 A:ILE23 4.5 16.9 0.8 C5 A:R8R201 4.5 13.8 0.1 CA A:VAL24 4.5 21.5 0.2 HB3 A:ALA52 4.6 12.4 0.2 CB A:ILE23 4.6 13.9 0.8 HD1 A:PHE156 4.6 28.9 0.8 HA A:VAL24 4.6 21.2 0.8 C9 A:R8R201 4.7 12.7 0.1 HB2 A:ALA52 4.7 14.1 0.8 CB A:ALA52 4.8 10.3 0.2 N A:GLU25 4.8 19.9 0.8 HB3 A:ASP22 4.8 26.6 0.2 N2 A:R8R202 4.9 12.2 0.1 HB2 A:PHE156 4.9 21.9 0.2 HB A:ILE23 4.9 16.7 0.8 CG1 A:VAL24 4.9 19.7 0.8 CD1 A:PHE156 4.9 24.1 0.8 C A:VAL24 5.0 18.1 0.8 CG A:PHE156 5.0 18.1 0.2

G.J.Correy, J.S.Fraser. Ligand Screen Against Sars-Cov-2 NSP3 Macrodomain To Be Published.