Fluorine in PDB 5srd: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5373433723 - (S) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5373433723 - (S) Isomer:
3.4.19.121;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5373433723 - (S) Isomer, PDB code: 5srd 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)	39.69 / 1.05
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.75, 88.75, 39.565, 90, 90, 90
R / Rfree (%)	14.7 / 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 Z5373433723 - (S) Isomer (pdb code 5srd). 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 Z5373433723 - (S) Isomer, PDB code: 5srd:
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 Z5373433723 - (S) 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 Z5373433723 - (S) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:14.1 occ:0.36 F17 A:R8K201 0.0 14.1 0.4 O A:HOH543 0.5 36.4 0.6 C14 A:R8K201 1.3 13.2 0.4 C15 A:R8K201 2.4 13.0 0.4 O A:HOH442 2.4 15.1 0.6 C13 A:R8K201 2.4 12.4 0.4 O A:HOH544 2.5 62.6 1.0 H151 A:R8K201 2.6 15.6 0.4 H131 A:R8K201 2.6 14.9 0.4 HB2 A:ALA52 2.6 14.2 0.6 O A:HOH535 2.7 39.3 0.6 O A:HOH451 2.8 35.9 0.6 HB2 A:ALA52 2.8 16.7 0.4 CB A:ALA52 3.4 11.9 0.6 HB1 A:ALA52 3.4 14.2 0.6 O A:HOH537 3.4 30.7 0.4 HB1 A:ALA52 3.5 16.7 0.4 CB A:ALA52 3.6 13.9 0.4 C12 A:R8K201 3.6 11.7 0.4 C16 A:R8K201 3.6 12.6 0.4 HB3 A:ALA52 4.0 14.2 0.6 O A:HOH538 4.1 31.7 0.6 HB3 A:ALA52 4.1 16.7 0.4 C11 A:R8K201 4.2 11.8 0.4 HA A:ALA52 4.2 12.3 0.6 CA A:ALA52 4.4 10.2 0.6 H161 A:R8K201 4.5 15.1 0.4 HA A:ALA52 4.5 15.9 0.4 HZ A:PHE156 4.6 19.3 0.4 CA A:ALA52 4.6 13.3 0.4 O A:GLY48 4.7 13.5 0.4 O A:GLY48 4.7 11.3 0.6 CZ A:PHE156 4.8 16.1 0.4 N18 A:R8K201 4.8 11.3 0.4 H A:ALA52 4.8 11.3 0.6 N A:ALA52 5.0 9.4 0.6

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5373433723 - (S) 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 Z5373433723 - (S) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:12.0 occ:0.36 F28 A:R8K201 0.0 12.0 0.4 O A:HOH453 0.4 17.3 0.6 C06 A:R8K201 1.3 12.1 0.4 H272 A:R8K201 2.3 14.4 0.4 C05 A:R8K201 2.3 13.1 0.4 C07 A:R8K201 2.4 12.0 0.4 C24 A:R8K201 2.4 11.9 0.4 H A:ILE131 2.5 14.7 0.6 H072 A:R8K201 2.5 14.4 0.4 HG12 A:ILE131 2.5 17.3 0.4 O A:HOH526 2.5 28.0 0.6 O29 A:R8K201 2.6 13.3 0.4 O A:HOH447 2.6 13.7 0.6 HA3 A:GLY130 2.7 15.8 0.6 C27 A:R8K201 2.8 12.0 0.4 HG12 A:ILE131 2.9 18.1 0.6 HA2 A:GLY48 2.9 14.4 0.6 H071 A:R8K201 2.9 14.4 0.4 HA3 A:GLY48 3.0 14.4 0.6 HD13 A:ILE131 3.1 18.0 0.4 HG23 A:ILE131 3.2 17.4 0.6 H A:VAL49 3.2 12.0 0.6 N A:ILE131 3.3 12.3 0.6 H252 A:R8K201 3.4 15.1 0.4 H A:ILE131 3.4 14.7 0.4 HG23 A:ILE131 3.4 16.0 0.4 CG1 A:ILE131 3.4 14.4 0.4 CA A:GLY48 3.4 12.0 0.6 C25 A:R8K201 3.4 12.6 0.4 H271 A:R8K201 3.5 14.4 0.4 HA2 A:GLY48 3.5 17.2 0.4 CD1 A:ILE131 3.6 15.0 0.4 N08 A:R8K201 3.6 11.9 0.4 HD11 A:ILE131 3.6 18.0 0.4 N04 A:R8K201 3.6 14.3 0.4 HA3 A:GLY48 3.6 17.2 0.4 CA A:GLY130 3.6 13.2 0.6 C23 A:R8K201 3.6 11.9 0.4 HG23 A:VAL49 3.7 15.2 0.6 H A:VAL49 3.7 15.8 0.4 H161 A:R8K201 3.8 15.1 0.4 H041 A:R8K201 3.8 17.1 0.4 C26 A:R8K201 3.8 12.3 0.4 CG1 A:ILE131 3.8 15.1 0.6 N A:VAL49 3.9 10.0 0.6 C A:GLY130 4.0 12.5 0.6 HA2 A:GLY130 4.0 15.8 0.6 CA A:GLY48 4.0 14.3 0.4 HG13 A:ILE131 4.0 17.3 0.4 CG2 A:ILE131 4.0 14.5 0.6 O A:HOH502 4.1 31.7 0.6 C A:GLY48 4.1 10.8 0.6 CG2 A:ILE131 4.1 13.3 0.4 N A:ILE131 4.2 12.2 0.4 HA3 A:GLY130 4.2 14.6 0.4 H261 A:R8K201 4.2 14.8 0.4 HD1 A:PHE132 4.3 15.9 0.4 CB A:ILE131 4.3 13.8 0.6 CB A:ILE131 4.3 13.3 0.4 O A:HOH418 4.3 12.1 0.6 CA A:ILE131 4.3 12.6 0.6 H232 A:R8K201 4.3 14.2 0.4 H231 A:R8K201 4.3 14.2 0.4 N A:VAL49 4.4 13.1 0.4 O A:ALA129 4.4 11.9 0.6 HD13 A:ILE131 4.4 19.8 0.6 HE1 A:PHE132 4.4 16.8 0.4 H251 A:R8K201 4.4 15.1 0.4 HG21 A:ILE131 4.4 16.0 0.4 HG13 A:ILE131 4.4 18.1 0.6 O A:HOH539 4.4 32.7 0.6 HD12 A:ILE131 4.5 18.0 0.4 HG21 A:ILE131 4.5 17.4 0.6 N A:GLY48 4.6 11.5 0.6 N A:GLY130 4.6 12.7 0.6 CD1 A:ILE131 4.6 16.5 0.6 H A:PHE132 4.6 13.6 0.6 HG22 A:ILE131 4.6 17.4 0.6 CG2 A:VAL49 4.7 12.6 0.6 C A:GLY48 4.7 13.6 0.4 HD1 A:PHE132 4.8 14.5 0.6 H262 A:R8K201 4.8 14.8 0.4 H012 A:R8K201 4.8 18.6 0.4 HB A:VAL49 4.8 16.6 0.4 H A:GLY48 4.8 13.8 0.6 C16 A:R8K201 4.8 12.6 0.4 HD11 A:ILE131 4.8 19.8 0.6 CA A:ILE131 4.8 12.6 0.4 C A:ALA129 4.9 11.6 0.6 O A:HOH413 4.9 13.7 0.4 C09 A:R8K201 4.9 11.7 0.4 O A:HOH343 4.9 17.3 0.6 HG22 A:ILE131 4.9 16.0 0.4 O A:HOH425 5.0 9.9 0.6 S02 A:R8K201 5.0 15.1 0.4 HA A:ILE131 5.0 15.1 0.6 CD1 A:PHE132 5.0 13.2 0.4

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