Fluorine in PDB 8f4s: Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16

The structure of Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16, PDB code: 8f4s was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases(Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.59 / 2.15
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	170.847, 170.847, 51.881, 90, 90, 120
R / Rfree (%)	16.6 / 19.1

The structure of Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 (pdb code 8f4s). 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 the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16, PDB code: 8f4s:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16


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 the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7102 b:89.2 occ:1.00 F3 A:XDU7102 0.0 89.2 1.0 C13 A:XDU7102 1.3 80.0 1.0 F2 A:XDU7102 2.2 72.3 1.0 F1 A:XDU7102 2.2 104.0 1.0 C12 A:XDU7102 2.3 68.8 1.0 CG2 A:THR6918 3.0 56.8 1.0 N2 A:XDU7102 3.0 60.7 1.0 C11 A:XDU7102 3.2 63.4 1.0 CD1 A:ILE6866 3.6 48.1 1.0 CB A:THR6918 3.6 59.3 1.0 CZ2 A:TRP6922 4.0 48.5 1.0 CE1 A:PHE6954 4.1 53.6 1.0 CD1 A:ILE7088 4.2 72.6 1.0 NE1 A:TRP6922 4.2 49.7 1.0 C1 A:XDU7102 4.2 64.8 1.0 CZ A:PHE6954 4.2 49.8 1.0 CG1 A:ILE7088 4.3 60.0 1.0 CE2 A:TRP6922 4.3 47.1 1.0 C2 A:XDU7102 4.4 69.2 1.0 CG2 A:ILE7088 4.5 64.6 1.0 OG1 A:THR6918 4.5 56.7 1.0 N A:THR6918 4.6 55.4 1.0 CA A:THR6918 4.7 58.7 1.0 CD1 A:LEU6909 4.7 80.8 1.0 N1 A:XDU7102 4.8 63.6 1.0 C A:HIS6917 4.8 60.3 1.0 CH2 A:TRP6922 4.9 45.8 1.0 CB A:ILE7088 5.0 58.8 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16


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 the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7102 b:104.0 occ:1.00 F1 A:XDU7102 0.0 104.0 1.0 C13 A:XDU7102 1.3 80.0 1.0 F3 A:XDU7102 2.2 89.2 1.0 F2 A:XDU7102 2.2 72.3 1.0 C12 A:XDU7102 2.3 68.8 1.0 N2 A:XDU7102 2.8 60.7 1.0 CG2 A:ILE7088 3.1 64.6 1.0 O A:HIS6917 3.3 58.1 1.0 C A:HIS6917 3.3 60.3 1.0 C11 A:XDU7102 3.4 63.4 1.0 CB A:THR6918 3.6 59.3 1.0 N A:HIS6917 3.6 57.9 1.0 N A:THR6918 3.7 55.4 1.0 CG2 A:THR6918 3.7 56.8 1.0 CA A:HIS6917 3.9 60.8 1.0 CD1 A:LEU6909 3.9 80.8 1.0 CG1 A:ILE7088 3.9 60.0 1.0 CB A:ILE7088 4.0 58.8 1.0 C1 A:XDU7102 4.1 64.8 1.0 CA A:THR6918 4.2 58.7 1.0 C A:VAL6916 4.2 59.1 1.0 CB A:VAL6916 4.2 62.3 1.0 CD1 A:ILE7088 4.3 72.6 1.0 CA A:ILE7088 4.4 54.9 1.0 C2 A:XDU7102 4.5 69.2 1.0 CG2 A:VAL6916 4.5 63.7 1.0 O A:SER7089 4.7 56.9 1.0 OG1 A:THR6918 4.7 56.7 1.0 CA A:VAL6916 4.8 60.4 1.0 N A:SER7089 4.8 56.6 1.0 O A:VAL6916 4.8 60.6 1.0 N1 A:XDU7102 4.8 63.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16


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 the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7102 b:72.3 occ:1.00 F2 A:XDU7102 0.0 72.3 1.0 C13 A:XDU7102 1.3 80.0 1.0 F3 A:XDU7102 2.2 89.2 1.0 F1 A:XDU7102 2.2 104.0 1.0 C12 A:XDU7102 2.3 68.8 1.0 C11 A:XDU7102 2.6 63.4 1.0 CD1 A:LEU6909 3.0 80.8 1.0 CD1 A:ILE6866 3.5 48.1 1.0 N2 A:XDU7102 3.6 60.7 1.0 C2 A:XDU7102 3.9 69.2 1.0 CG2 A:ILE7088 4.1 64.6 1.0 CG2 A:VAL6916 4.2 63.7 1.0 CB A:VAL6916 4.4 62.3 1.0 CD1 A:ILE7088 4.4 72.6 1.0 CG A:LEU6909 4.4 69.9 1.0 C3 A:XDU7102 4.6 73.8 1.0 C1 A:XDU7102 4.6 64.8 1.0 N1 A:XDU7102 4.8 63.6 1.0 CG1 A:ILE7088 4.8 60.0 1.0 CG1 A:ILE6866 4.8 45.5 1.0 CE1 A:PHE6868 4.9 58.4 1.0 CG2 A:THR6918 5.0 56.8 1.0

N.L.Inniss, J.Kozic, F.Li, M.Rosas-Lemus, G.Minasov, J.Rybacek, Y.Zhu, R.Pohl, L.Shuvalova, L.Rulisek, J.S.Brunzelle, L.Bednarova, M.Stefek, J.M.Kormanik, E.Andris, J.Sebestik, A.S.M.Li, P.J.Brown, U.Schmitz, K.Saikatendu, E.Chang, R.Nencka, M.Vedadi, K.J.F.Satchell. Discovery of A Druggable, Cryptic Pocket in Sars-Cov-2 NSP16 Using Allosteric Inhibitors. Acs Infect Dis. 2023.
ISSN: ESSN 2373-8227
PubMed: 37728236
DOI: 10.1021/ACSINFECDIS.3C00203