Fluorine in PDB 5rv1: Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000251609

All present enzymatic activity of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000251609:
3.4.19.12;

The structure of Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000251609, PDB code: 5rv1 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)	39.63 / 1.00
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.624, 88.624, 39.312, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000251609 (pdb code 5rv1). 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 ZINC000000251609, PDB code: 5rv1:
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 ZINC000000251609


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 ZINC000000251609 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:25.8 occ:1.00 F1 A:TFA201 0.0 25.8 1.0 C2 A:TFA201 1.3 24.1 1.0 F2 A:TFA201 2.0 25.7 1.0 F3 A:TFA201 2.0 26.2 1.0 C1 A:TFA201 2.3 20.2 1.0 OXT A:TFA201 2.8 17.6 1.0 HD21 A:LEU160 2.9 23.6 1.0 HD23 A:LEU160 3.0 23.6 1.0 HB1 A:ALA129 3.0 19.8 1.0 HB3 A:ALA129 3.1 19.8 1.0 O A:TFA201 3.1 20.5 1.0 HD12 A:LEU126 3.2 18.6 1.0 HB2 A:LEU126 3.2 15.0 1.0 CD2 A:LEU160 3.3 19.6 1.0 HB3 A:PRO136 3.4 19.5 1.0 CB A:ALA129 3.5 16.4 1.0 O A:HOH392 3.5 13.8 1.0 HG13 A:VAL155 3.6 18.9 1.0 HD22 A:LEU160 3.7 23.6 1.0 H A:GLY130 3.9 18.1 1.0 HB2 A:ALA129 4.0 19.8 1.0 CD1 A:LEU126 4.0 15.5 1.0 HD13 A:LEU126 4.1 18.6 1.0 CB A:LEU126 4.2 12.5 1.0 HB2 A:PRO136 4.2 19.5 1.0 CB A:PRO136 4.2 16.2 1.0 O A:HOH334 4.3 18.9 1.0 N A:GLY130 4.3 15.1 1.0 HB3 A:LEU126 4.4 15.0 1.0 HA A:VAL155 4.4 18.0 1.0 O A:HOH383 4.5 17.0 1.0 HD11 A:LEU164 4.5 19.6 1.0 H A:LEU126 4.5 13.9 1.0 CG1 A:VAL155 4.5 15.7 1.0 O A:HOH345 4.6 18.0 1.0 CG A:LEU126 4.6 13.8 1.0 H A:PHE156 4.6 19.3 1.0 CG A:LEU160 4.7 19.9 1.0 HG A:LEU160 4.7 23.9 1.0 HG3 A:PRO136 4.7 20.8 1.0 HD11 A:LEU126 4.7 18.6 1.0 CA A:ALA129 4.7 15.2 1.0 C A:ALA129 4.8 14.7 1.0 HG A:LEU126 4.8 16.5 1.0 HG12 A:VAL155 4.8 18.9 1.0 HA3 A:GLY130 4.8 19.0 1.0 O A:HOH401 4.9 27.8 1.0 HA2 A:GLY130 4.9 19.0 1.0 HG22 A:VAL155 4.9 19.2 1.0 CA A:GLY130 5.0 15.8 1.0 O A:LEU126 5.0 12.4 1.0 HG11 A:VAL155 5.0 18.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000251609


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 ZINC000000251609 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:25.7 occ:1.00 F2 A:TFA201 0.0 25.7 1.0 C2 A:TFA201 1.2 24.1 1.0 F3 A:TFA201 2.0 26.2 1.0 F1 A:TFA201 2.0 25.8 1.0 C1 A:TFA201 2.4 20.2 1.0 O A:TFA201 2.6 20.5 1.0 HD23 A:LEU160 2.8 23.6 1.0 HD22 A:LEU160 2.9 23.6 1.0 H A:GLY130 3.0 18.1 1.0 HD21 A:LEU160 3.1 23.6 1.0 CD2 A:LEU160 3.1 19.6 1.0 O A:HOH334 3.2 18.9 1.0 O A:HOH401 3.2 27.8 1.0 HA2 A:GLY130 3.3 19.0 1.0 HB1 A:ALA129 3.4 19.8 1.0 N A:GLY130 3.4 15.1 1.0 OXT A:TFA201 3.4 17.6 1.0 HA3 A:GLY130 3.7 19.0 1.0 CA A:GLY130 3.7 15.8 1.0 HB3 A:ALA129 4.0 19.8 1.0 HB3 A:PRO136 4.0 19.5 1.0 CB A:ALA129 4.1 16.4 1.0 C A:ALA129 4.4 14.7 1.0 HG3 A:PRO136 4.4 20.8 1.0 HB3 A:ASP157 4.5 24.3 1.0 HB2 A:ASP157 4.5 24.3 1.0 CG A:LEU160 4.6 19.9 1.0 HG13 A:VAL155 4.7 18.9 1.0 H A:ASP157 4.7 22.6 1.0 O A:HOH491 4.8 24.1 1.0 CB A:PRO136 4.8 16.2 1.0 HB2 A:ALA129 4.9 19.8 1.0 O A:HOH383 4.9 17.0 1.0 CA A:ALA129 4.9 15.2 1.0 HB3 A:LEU160 5.0 22.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with ZINC000000251609


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 ZINC000000251609 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:26.2 occ:1.00 F3 A:TFA201 0.0 26.2 1.0 C2 A:TFA201 1.2 24.1 1.0 F2 A:TFA201 2.0 25.7 1.0 F1 A:TFA201 2.0 25.8 1.0 C1 A:TFA201 2.3 20.2 1.0 OXT A:TFA201 2.8 17.6 1.0 HA3 A:GLY130 3.2 19.0 1.0 O A:HOH383 3.2 17.0 1.0 HB3 A:ALA129 3.2 19.8 1.0 O A:TFA201 3.2 20.5 1.0 H A:GLY130 3.3 18.1 1.0 N A:GLY130 3.4 15.1 1.0 O A:HOH345 3.4 18.0 1.0 HB1 A:ALA129 3.5 19.8 1.0 CA A:GLY130 3.6 15.8 1.0 O A:HOH491 3.7 24.1 1.0 HA2 A:GLY130 3.7 19.0 1.0 CB A:ALA129 3.8 16.4 1.0 O A:HOH401 3.8 27.8 1.0 C A:ALA129 3.9 14.7 1.0 O A:HOH392 4.1 13.8 1.0 HB2 A:LEU126 4.2 15.0 1.0 HD23 A:LEU160 4.3 23.6 1.0 O A:ALA129 4.4 14.5 1.0 O A:HOH334 4.4 18.9 1.0 CA A:ALA129 4.5 15.2 1.0 O A:HOH450 4.5 21.5 1.0 HD21 A:LEU160 4.6 23.6 1.0 HB2 A:ALA129 4.6 19.8 1.0 H A:PHE156 4.7 19.3 1.0 O A:LEU126 4.8 12.4 1.0 O A:HOH472 4.8 40.3 1.0 CD2 A:LEU160 4.8 19.6 1.0 HD22 A:LEU160 4.8 23.6 1.0 HB3 A:PHE156 4.8 22.7 1.0 HB3 A:PRO136 4.8 19.5 1.0 H A:LEU126 4.9 13.9 1.0 HD12 A:LEU126 5.0 18.6 1.0

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