Fluorine in PDB 5sra: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5372052920 - (R) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5372052920 - (R) Isomer:
3.4.19.121;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5372052920 - (R) Isomer, PDB code: 5sra 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)	39.67 / 1.05
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.702, 88.702, 39.329, 90, 90, 90
R / Rfree (%)	13.8 / 15.7

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5372052920 - (R) Isomer (pdb code 5sra). 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 Z5372052920 - (R) Isomer, PDB code: 5sra:
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 Z5372052920 - (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 Z5372052920 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:11.1 occ:0.15 F14 A:R0L201 0.0 11.1 0.1 F14 A:R0L202 0.0 10.3 0.1 O A:HOH558 1.3 36.2 0.7 C11 A:R0L202 1.4 10.2 0.1 C11 A:R0L201 1.4 11.1 0.1 O A:HOH442 1.4 16.2 0.7 C10 A:R0L202 2.4 10.3 0.1 C10 A:R0L201 2.4 11.2 0.1 C12 A:R0L201 2.4 10.8 0.1 C12 A:R0L202 2.4 9.8 0.1 HB2 A:ALA52 2.5 13.1 0.3 HB2 A:ALA52 2.6 14.3 0.7 H101 A:R0L202 2.6 12.4 0.1 H121 A:R0L201 2.6 12.9 0.1 H121 A:R0L202 2.6 11.8 0.1 H101 A:R0L201 2.6 13.4 0.1 O A:HOH555 3.1 14.7 0.3 O A:HOH466 3.3 45.1 0.7 CB A:ALA52 3.3 10.9 0.3 HB1 A:ALA52 3.4 13.1 0.3 CB A:ALA52 3.5 12.0 0.7 O A:HOH544 3.5 36.8 0.7 O A:HOH546 3.5 30.6 0.7 C09 A:R0L202 3.6 10.4 0.1 C13 A:R0L202 3.7 10.0 0.1 C09 A:R0L201 3.7 11.4 0.1 C13 A:R0L201 3.7 11.0 0.1 HB3 A:ALA52 3.7 13.1 0.3 HB1 A:ALA52 3.7 14.3 0.7 O A:HOH539 3.8 28.2 0.3 HB3 A:ALA52 3.9 14.3 0.7 O A:GLY48 4.1 11.8 0.7 C08 A:R0L201 4.1 11.7 0.1 C08 A:R0L202 4.2 10.7 0.1 O A:GLY48 4.2 13.7 0.3 O A:HOH327 4.2 25.3 0.3 HA A:ALA52 4.4 12.6 0.7 CA A:ALA52 4.5 10.5 0.7 H131 A:R0L202 4.5 12.1 0.1 H131 A:R0L201 4.5 13.2 0.1 H A:ALA52 4.5 11.7 0.7 CA A:ALA52 4.5 10.7 0.3 HA A:ALA52 4.6 12.8 0.3 H A:ALA52 4.6 13.2 0.3 HA2 A:GLY48 4.7 16.6 0.3 C A:GLY48 4.7 13.5 0.3 N A:ALA52 4.8 9.8 0.7 C A:GLY48 4.8 11.4 0.7 O A:HOH513 4.8 36.4 0.7 N15 A:R0L202 4.8 10.3 0.1 N15 A:R0L201 4.9 11.3 0.1 N A:ALA52 4.9 11.0 0.3 HA2 A:GLY48 4.9 14.7 0.7

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5372052920 - (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 Z5372052920 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:10.3 occ:0.15 F14 A:R0L202 0.0 10.3 0.1 F14 A:R0L201 0.0 11.1 0.1 O A:HOH558 1.3 36.2 0.7 C11 A:R0L202 1.4 10.2 0.1 C11 A:R0L201 1.4 11.1 0.1 O A:HOH442 1.4 16.2 0.7 C10 A:R0L202 2.4 10.3 0.1 C10 A:R0L201 2.4 11.2 0.1 C12 A:R0L201 2.4 10.8 0.1 C12 A:R0L202 2.4 9.8 0.1 HB2 A:ALA52 2.5 13.1 0.3 HB2 A:ALA52 2.6 14.3 0.7 H121 A:R0L201 2.6 12.9 0.1 H121 A:R0L202 2.6 11.8 0.1 H101 A:R0L202 2.6 12.4 0.1 H101 A:R0L201 2.6 13.4 0.1 O A:HOH555 3.1 14.7 0.3 O A:HOH466 3.3 45.1 0.7 CB A:ALA52 3.3 10.9 0.3 HB1 A:ALA52 3.4 13.1 0.3 CB A:ALA52 3.5 12.0 0.7 O A:HOH544 3.5 36.8 0.7 O A:HOH546 3.5 30.6 0.7 C09 A:R0L202 3.6 10.4 0.1 C13 A:R0L202 3.7 10.0 0.1 C13 A:R0L201 3.7 11.0 0.1 C09 A:R0L201 3.7 11.4 0.1 HB3 A:ALA52 3.7 13.1 0.3 HB1 A:ALA52 3.7 14.3 0.7 O A:HOH539 3.8 28.2 0.3 HB3 A:ALA52 3.9 14.3 0.7 O A:GLY48 4.1 11.8 0.7 C08 A:R0L201 4.2 11.7 0.1 C08 A:R0L202 4.2 10.7 0.1 O A:GLY48 4.2 13.7 0.3 O A:HOH327 4.2 25.3 0.3 HA A:ALA52 4.4 12.6 0.7 CA A:ALA52 4.5 10.5 0.7 H131 A:R0L202 4.5 12.1 0.1 H131 A:R0L201 4.5 13.2 0.1 H A:ALA52 4.5 11.7 0.7 CA A:ALA52 4.5 10.7 0.3 HA A:ALA52 4.6 12.8 0.3 H A:ALA52 4.6 13.2 0.3 HA2 A:GLY48 4.7 16.6 0.3 C A:GLY48 4.7 13.5 0.3 N A:ALA52 4.8 9.8 0.7 C A:GLY48 4.8 11.4 0.7 O A:HOH513 4.8 36.4 0.7 N15 A:R0L202 4.8 10.3 0.1 N15 A:R0L201 4.9 11.3 0.1 HA2 A:GLY48 4.9 14.7 0.7 N A:ALA52 4.9 11.0 0.3

S.Gahbauer, G.J.Correy, M.Schuller, M.P.Ferla, Y.U.Doruk, M.Rachman, T.Wu, M.Diolaiti, S.Wang, R.J.Neitz, D.Fearon, D.Radchenko, Y.Moroz, J.J.Irwin, A.R.Renslo, J.C.Taylor, J.E.Gestwicki, F.Von Delft, A.Ashworth, I.Ahel, B.K.Shoichet, J.S.Fraser. Structure-Based Inhibitor Optimization For the NSP3 Macrodomain of Sars-Cov-2. Biorxiv 2022.
ISSN: ISSN 2692-8205
PubMed: 35794891
DOI: 10.1101/2022.06.27.497816