Fluorine in PDB 5rup: Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927

All present enzymatic activity of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927:
3.4.19.12;

The structure of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927, PDB code: 5rup was solved by G.J.Correy, I.D.Young, M.C.Thompson, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.65 / 1.00
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.669, 88.669, 39.362, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 17.4

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927 (pdb code 5rup). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927, PDB code: 5rup:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:20.6 occ:0.62 F1 A:04R201 0.0 20.6 0.6 C2 A:04R201 1.3 20.1 0.6 F3 A:04R201 2.2 21.3 0.6 F4 A:04R201 2.2 21.2 0.6 C5 A:04R201 2.3 17.7 0.6 HG3 A:PRO136 2.5 22.3 1.0 HD22 A:LEU160 3.0 24.2 1.0 H10 A:04R201 3.1 22.1 0.6 C9 A:04R201 3.1 17.4 0.6 HD13 A:LEU160 3.2 25.6 1.0 HD3 A:PRO136 3.3 21.3 1.0 N6 A:04R201 3.3 17.0 0.6 CG A:PRO136 3.3 18.6 1.0 C10 A:04R201 3.5 18.4 0.6 CD A:PRO136 3.7 17.7 1.0 H10A A:04R201 3.8 22.1 0.6 CD2 A:LEU160 3.8 20.1 1.0 HG2 A:PRO136 3.8 22.3 1.0 HD21 A:LEU160 3.8 24.2 1.0 HD2 A:PRO136 3.8 21.3 1.0 CD1 A:LEU160 4.1 21.3 1.0 C8 A:04R201 4.3 17.1 0.6 N A:04R201 4.3 16.2 0.6 HB3 A:PRO136 4.3 21.0 1.0 CB A:PRO136 4.5 17.5 1.0 HD23 A:LEU160 4.5 24.2 1.0 H A:GLY130 4.5 19.7 1.0 CG A:LEU160 4.5 20.6 1.0 HD11 A:LEU160 4.5 25.6 1.0 HB2 A:LEU160 4.6 26.1 1.0 HD12 A:LEU160 4.8 25.6 1.0 C11 A:04R201 4.9 18.8 0.6 HB2 A:PRO136 5.0 21.0 1.0 HB1 A:ALA129 5.0 17.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:21.3 occ:0.62 F3 A:04R201 0.0 21.3 0.6 C2 A:04R201 1.3 20.1 0.6 F4 A:04R201 2.1 21.2 0.6 F1 A:04R201 2.2 20.6 0.6 C5 A:04R201 2.3 17.7 0.6 H10A A:04R201 3.0 22.1 0.6 C9 A:04R201 3.0 17.4 0.6 C10 A:04R201 3.3 18.4 0.6 H10 A:04R201 3.3 22.1 0.6 N6 A:04R201 3.3 17.0 0.6 H A:GLY130 3.8 19.7 1.0 HD3 A:PRO136 3.9 21.3 1.0 HA2 A:GLY130 4.1 21.6 1.0 C8 A:04R201 4.2 17.1 0.6 HG3 A:PRO136 4.2 22.3 1.0 N A:04R201 4.3 16.2 0.6 O A:GLY130 4.4 18.4 1.0 N A:GLY130 4.4 16.4 1.0 HD22 A:LEU160 4.6 24.2 1.0 CA A:GLY130 4.6 18.0 1.0 CD A:PRO136 4.7 17.7 1.0 C11 A:04R201 4.8 18.8 0.6 O A:ALA134 4.9 14.9 1.0 CG A:PRO136 4.9 18.6 1.0 HD2 A:PRO136 4.9 21.3 1.0 C A:GLY130 5.0 18.5 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000004976927 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:21.2 occ:0.62 F4 A:04R201 0.0 21.2 0.6 C2 A:04R201 1.4 20.1 0.6 F3 A:04R201 2.1 21.3 0.6 F1 A:04R201 2.2 20.6 0.6 HD3 A:PRO136 2.2 21.3 1.0 C5 A:04R201 2.4 17.7 0.6 HG3 A:PRO136 2.7 22.3 1.0 N6 A:04R201 2.7 17.0 0.6 H A:GLY130 2.9 19.7 1.0 CD A:PRO136 3.0 17.7 1.0 CG A:PRO136 3.2 18.6 1.0 HB1 A:ALA129 3.4 17.4 1.0 HB3 A:PRO136 3.4 21.0 1.0 O A:ALA134 3.5 14.9 1.0 HA A:ALA129 3.6 16.7 1.0 HD2 A:PRO136 3.6 21.3 1.0 N A:GLY130 3.7 16.4 1.0 C9 A:04R201 3.7 17.4 0.6 CB A:PRO136 3.8 17.5 1.0 HD22 A:LEU160 3.9 24.2 1.0 N A:04R201 4.0 16.2 0.6 HD21 A:LEU160 4.0 24.2 1.0 N A:PRO136 4.0 16.6 1.0 HG2 A:PRO136 4.1 22.3 1.0 CB A:ALA129 4.1 14.5 1.0 CA A:ALA129 4.2 13.9 1.0 HA2 A:GLY130 4.3 21.6 1.0 HB2 A:ALA129 4.4 17.4 1.0 C A:ALA129 4.4 15.5 1.0 CD2 A:LEU160 4.4 20.1 1.0 C8 A:04R201 4.5 17.1 0.6 HA A:ASP135 4.5 20.5 1.0 CA A:PRO136 4.6 16.6 1.0 CA A:GLY130 4.6 18.0 1.0 HD13 A:LEU160 4.6 25.6 1.0 H10 A:04R201 4.6 22.1 0.6 HB2 A:PRO136 4.6 21.0 1.0 C10 A:04R201 4.6 18.4 0.6 H10A A:04R201 4.7 22.1 0.6 O A:GLY130 4.7 18.4 1.0 C A:ALA134 4.7 13.9 1.0 HA A:PRO136 4.7 19.9 1.0 H14 A:04R201 4.9 19.3 0.6 HB3 A:ALA129 4.9 17.4 1.0 C A:ASP135 5.0 16.5 1.0 HD23 A:LEU160 5.0 24.2 1.0

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