Fluorine in PDB 5srv: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562533 - (R,R) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562533 - (R,R) Isomer:
3.4.19.121;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562533 - (R,R) Isomer, PDB code: 5srv 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)	39.72 / 1.05
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.825, 88.825, 39.598, 90, 90, 90
R / Rfree (%)	14.4 / 16.5

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562533 - (R,R) Isomer (pdb code 5srv). 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 Z5198562533 - (R,R) Isomer, PDB code: 5srv:
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 Z5198562533 - (R,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 Z5198562533 - (R,R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:15.2 occ:0.24 F14 A:RI3201 0.0 15.2 0.2 O A:HOH550 0.9 40.9 0.8 C11 A:RI3201 1.4 14.5 0.2 O A:HOH448 1.8 17.6 0.8 C10 A:RI3201 2.4 13.7 0.2 C12 A:RI3201 2.4 14.5 0.2 HB2 A:ALA52 2.6 13.4 0.2 H121 A:RI3201 2.6 17.5 0.2 H101 A:RI3201 2.6 16.4 0.2 HB2 A:ALA52 2.6 16.1 0.8 O A:HOH548 2.8 56.4 1.0 O A:HOH464 3.0 46.6 0.8 HB1 A:ALA52 3.3 13.4 0.2 CB A:ALA52 3.3 11.1 0.2 O A:HOH491 3.5 43.7 1.0 CB A:ALA52 3.5 13.4 0.8 HB1 A:ALA52 3.6 16.1 0.8 C13 A:RI3201 3.7 14.6 0.2 C09 A:RI3201 3.7 13.6 0.2 O A:HOH536 3.7 40.0 0.8 HB3 A:ALA52 3.8 13.4 0.2 HB3 A:ALA52 4.0 16.1 0.8 C08 A:RI3201 4.2 14.3 0.2 HA A:ALA52 4.4 14.6 0.8 HE2 A:PHE156 4.4 26.6 0.2 HA A:ALA52 4.4 12.7 0.2 O A:GLY48 4.4 12.0 0.8 CA A:ALA52 4.5 12.2 0.8 H131 A:RI3201 4.5 17.5 0.2 CA A:ALA52 4.5 10.6 0.2 O A:GLY48 4.5 13.9 0.2 H A:ALA52 4.7 13.3 0.8 CE2 A:PHE156 4.8 22.2 0.2 H A:ALA52 4.8 12.1 0.2 N15 A:RI3201 4.8 13.3 0.2 HA A:VAL49 4.9 16.9 0.2 N A:ALA52 4.9 11.1 0.8 HZ A:PHE156 5.0 26.9 0.2

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5198562533 - (R,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 Z5198562533 - (R,R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:20.6 occ:0.24 F25 A:RI3201 0.0 20.6 0.2 C03 A:RI3201 1.3 19.9 0.2 O A:HOH531 1.6 29.9 0.8 O A:HOH512 1.9 35.3 0.8 HA3 A:GLY130 1.9 15.9 0.8 C02 A:RI3201 2.3 20.2 0.2 C21 A:RI3201 2.4 19.8 0.2 C04 A:RI3201 2.4 19.1 0.2 HA3 A:GLY130 2.5 15.3 0.2 H221 A:RI3201 2.6 23.7 0.2 H041 A:RI3201 2.6 22.9 0.2 N05 A:RI3201 2.7 18.0 0.2 O26 A:RI3201 2.7 20.2 0.2 O A:HOH439 2.7 16.4 0.8 CA A:GLY130 2.8 13.3 0.8 C20 A:RI3201 2.8 19.3 0.2 C22 A:RI3201 2.8 19.7 0.2 H201 A:RI3201 2.9 23.2 0.2 HA2 A:GLY130 2.9 15.9 0.8 N A:GLY130 3.2 13.0 0.8 H211 A:RI3201 3.3 23.8 0.2 H042 A:RI3201 3.3 22.9 0.2 CA A:GLY130 3.4 12.7 0.2 O01 A:RI3201 3.5 20.4 0.2 H A:GLY130 3.5 15.6 0.8 O A:HOH374 3.7 19.7 0.8 O A:HOH545 3.7 35.6 0.8 H A:ILE131 3.7 15.6 0.8 HA2 A:GLY130 3.7 15.3 0.2 C24 A:RI3201 3.7 19.8 0.2 C A:ALA129 3.8 11.6 0.8 N A:GLY130 3.8 12.6 0.2 H202 A:RI3201 3.9 23.2 0.2 H A:ILE131 3.9 15.3 0.2 HG23 A:VAL49 3.9 17.9 0.8 O A:ALA129 3.9 11.6 0.8 H241 A:RI3201 4.0 23.8 0.2 C A:GLY130 4.0 12.9 0.8 H242 A:RI3201 4.0 23.8 0.2 C06 A:RI3201 4.1 15.8 0.2 O A:HOH453 4.2 13.8 0.8 HB3 A:ALA129 4.2 16.3 0.8 H A:GLY130 4.2 15.1 0.2 N A:ILE131 4.2 13.0 0.8 O A:HOH470 4.2 21.1 0.8 C A:ALA129 4.3 13.0 0.2 H131 A:RI3201 4.3 17.5 0.2 O A:ALA129 4.3 14.1 0.2 C23 A:RI3201 4.3 19.6 0.2 HB1 A:ALA129 4.4 16.3 0.8 O A:HOH416 4.4 13.2 0.8 HB3 A:ALA129 4.5 14.7 0.2 N A:ILE131 4.5 12.7 0.2 C A:GLY130 4.5 13.1 0.2 CB A:ALA129 4.6 13.6 0.8 O A:HOH365 4.7 27.1 1.0 HG12 A:ILE131 4.7 20.0 0.2 CG2 A:VAL49 4.7 14.9 0.8 CA A:ALA129 4.8 12.0 0.8 H A:VAL49 4.8 13.7 0.8 HG21 A:VAL49 4.8 17.9 0.8 N19 A:RI3201 4.8 15.2 0.2 O A:HOH310 4.9 28.1 1.0 H232 A:RI3201 4.9 23.6 0.2 H231 A:RI3201 4.9 23.6 0.2

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