Fluorine in PDB 8f4y: Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10

The structure of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10, PDB code: 8f4y 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)	29.62 / 2.13
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.04, 171.04, 52.029, 90, 90, 120
R / Rfree (%)	15.7 / 18

The structure of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 also contains other interesting chemical elements:

Chlorine	(Cl)	8 atoms
Zinc	(Zn)	2 atoms
Sodium	(Na)	2 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 (pdb code 8f4y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10, PDB code: 8f4y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


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 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7102 b:71.7 occ:0.50 F3 A:XDU7102 0.0 71.7 0.5 F2 A:XE07103 0.3 69.1 0.5 C13 A:XE07103 1.3 60.3 0.5 C13 A:XDU7102 1.3 65.7 0.5 F3 A:XE07103 1.9 72.4 0.5 F2 A:XDU7102 2.1 61.8 0.5 F1 A:XDU7102 2.2 72.7 0.5 F1 A:XE07103 2.2 60.8 0.5 C12 A:XE07103 2.2 52.2 0.5 C12 A:XDU7102 2.3 62.2 0.5 N2 A:XE07103 2.9 46.9 0.5 CG2 A:THR6918 3.0 50.2 1.0 N2 A:XDU7102 3.0 60.5 0.5 C11 A:XDU7102 3.2 62.0 0.5 C11 A:XE07103 3.2 46.9 0.5 CB A:THR6918 3.3 52.4 1.0 CD1 A:ILE7088 3.8 66.6 1.0 CG1 A:ILE7088 3.8 54.5 1.0 CD1 A:ILE6866 3.8 42.8 1.0 CZ2 A:TRP6922 3.9 45.3 1.0 C1 A:XE07103 4.2 45.9 0.5 OG1 A:THR6918 4.2 51.2 1.0 CG2 A:ILE7088 4.2 59.9 1.0 C1 A:XDU7102 4.2 64.7 0.5 NE1 A:TRP6922 4.3 43.6 1.0 CE2 A:TRP6922 4.3 43.0 1.0 C2 A:XDU7102 4.4 69.9 0.5 C2 A:XE07103 4.4 46.5 0.5 CE1 A:PHE6954 4.4 46.1 1.0 N A:THR6918 4.5 49.0 1.0 CA A:THR6918 4.5 51.5 1.0 CZ A:PHE6954 4.6 43.9 1.0 CB A:ILE7088 4.6 55.1 1.0 C A:HIS6917 4.6 55.6 1.0 O A:HIS6917 4.8 54.2 1.0 CH2 A:TRP6922 4.8 42.3 1.0 N1 A:XE07103 4.8 45.6 0.5 N1 A:XDU7102 4.8 64.0 0.5

Fluorine binding site 2 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


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 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7102 b:72.7 occ:0.50 F1 A:XDU7102 0.0 72.7 0.5 F3 A:XE07103 0.3 72.4 0.5 C13 A:XDU7102 1.3 65.7 0.5 C13 A:XE07103 1.6 60.3 0.5 F2 A:XDU7102 2.2 61.8 0.5 F3 A:XDU7102 2.2 71.7 0.5 C12 A:XDU7102 2.3 62.2 0.5 F2 A:XE07103 2.4 69.1 0.5 F1 A:XE07103 2.4 60.8 0.5 C12 A:XE07103 2.5 52.2 0.5 N2 A:XE07103 2.8 46.9 0.5 N2 A:XDU7102 2.8 60.5 0.5 CG2 A:ILE7088 2.8 59.9 1.0 O A:HIS6917 3.0 54.2 1.0 C A:HIS6917 3.2 55.6 1.0 C11 A:XDU7102 3.4 62.0 0.5 CB A:THR6918 3.5 52.4 1.0 N A:HIS6917 3.6 53.3 1.0 N A:THR6918 3.6 49.0 1.0 CB A:ILE7088 3.6 55.1 1.0 CG1 A:ILE7088 3.6 54.5 1.0 C11 A:XE07103 3.7 46.9 0.5 CA A:HIS6917 3.8 58.4 1.0 CG2 A:THR6918 3.8 50.2 1.0 CA A:ILE7088 4.0 51.1 1.0 CA A:THR6918 4.0 51.5 1.0 CD1 A:ILE7088 4.1 66.6 1.0 C1 A:XE07103 4.1 45.9 0.5 C1 A:XDU7102 4.1 64.7 0.5 C A:VAL6916 4.3 56.2 1.0 N A:SER7089 4.4 52.4 1.0 CB A:VAL6916 4.4 60.5 1.0 O A:SER7089 4.4 55.5 1.0 OG1 A:THR6918 4.5 51.2 1.0 C2 A:XDU7102 4.6 69.9 0.5 C A:ILE7088 4.7 52.3 1.0 C2 A:XE07103 4.7 46.5 0.5 CG2 A:VAL6916 4.8 59.4 1.0 CA A:VAL6916 4.8 56.5 1.0 N1 A:XDU7102 4.9 64.0 0.5 O A:XE07103 4.9 42.0 0.5 N1 A:XE07103 4.9 45.6 0.5 O A:VAL6916 5.0 57.4 1.0 O1 A:XDU7102 5.0 67.1 0.5

Fluorine binding site 3 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


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 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7102 b:61.8 occ:0.50 F2 A:XDU7102 0.0 61.8 0.5 F1 A:XE07103 0.3 60.8 0.5 C13 A:XE07103 1.2 60.3 0.5 C13 A:XDU7102 1.3 65.7 0.5 F3 A:XE07103 1.9 72.4 0.5 F2 A:XE07103 2.1 69.1 0.5 F3 A:XDU7102 2.1 71.7 0.5 F1 A:XDU7102 2.2 72.7 0.5 C12 A:XDU7102 2.3 62.2 0.5 C12 A:XE07103 2.3 52.2 0.5 C11 A:XDU7102 2.6 62.0 0.5 C11 A:XE07103 2.7 46.9 0.5 N2 A:XE07103 3.5 46.9 0.5 N2 A:XDU7102 3.5 60.5 0.5 CG2 A:ILE7088 3.6 59.9 1.0 CD1 A:ILE6866 3.9 42.8 1.0 C2 A:XDU7102 4.0 69.9 0.5 CD1 A:ILE7088 4.0 66.6 1.0 CG A:LEU6909 4.1 64.3 1.0 C2 A:XE07103 4.1 46.5 0.5 CD2 A:LEU6909 4.1 75.6 1.0 CG2 A:VAL6916 4.3 59.4 1.0 CB A:VAL6916 4.3 60.5 1.0 CG1 A:ILE7088 4.3 54.5 1.0 C1 A:XE07103 4.6 45.9 0.5 C1 A:XDU7102 4.6 64.7 0.5 CB A:ILE7088 4.6 55.1 1.0 C3 A:XDU7102 4.7 77.8 0.5 N1 A:XDU7102 4.8 64.0 0.5 CB A:LEU6909 4.8 55.9 1.0 N1 A:XE07103 4.9 45.6 0.5 CG1 A:VAL6894 4.9 42.8 1.0 CG2 A:THR6918 4.9 50.2 1.0 C3 A:XE07103 5.0 49.9 0.5 N A:HIS6917 5.0 53.3 1.0

Fluorine binding site 4 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7103 b:72.4 occ:0.50 F3 A:XE07103 0.0 72.4 0.5 F1 A:XDU7102 0.3 72.7 0.5 C13 A:XDU7102 1.0 65.7 0.5 C13 A:XE07103 1.3 60.3 0.5 F2 A:XDU7102 1.9 61.8 0.5 F3 A:XDU7102 1.9 71.7 0.5 C12 A:XDU7102 2.1 62.2 0.5 F2 A:XE07103 2.2 69.1 0.5 F1 A:XE07103 2.2 60.8 0.5 C12 A:XE07103 2.3 52.2 0.5 N2 A:XE07103 2.7 46.9 0.5 N2 A:XDU7102 2.8 60.5 0.5 CG2 A:ILE7088 2.9 59.9 1.0 C11 A:XDU7102 3.2 62.0 0.5 O A:HIS6917 3.3 54.2 1.0 C A:HIS6917 3.4 55.6 1.0 C11 A:XE07103 3.4 46.9 0.5 CB A:THR6918 3.5 52.4 1.0 CG1 A:ILE7088 3.6 54.5 1.0 CB A:ILE7088 3.7 55.1 1.0 CG2 A:THR6918 3.8 50.2 1.0 N A:THR6918 3.8 49.0 1.0 N A:HIS6917 3.8 53.3 1.0 CD1 A:ILE7088 4.0 66.6 1.0 CA A:HIS6917 4.0 58.4 1.0 C1 A:XE07103 4.1 45.9 0.5 C1 A:XDU7102 4.1 64.7 0.5 CA A:THR6918 4.2 51.5 1.0 CA A:ILE7088 4.2 51.1 1.0 CB A:VAL6916 4.4 60.5 1.0 C2 A:XDU7102 4.4 69.9 0.5 C A:VAL6916 4.4 56.2 1.0 C2 A:XE07103 4.6 46.5 0.5 OG1 A:THR6918 4.6 51.2 1.0 N A:SER7089 4.6 52.4 1.0 O A:SER7089 4.7 55.5 1.0 CG2 A:VAL6916 4.7 59.4 1.0 N1 A:XDU7102 4.8 64.0 0.5 N1 A:XE07103 4.8 45.6 0.5 O A:XE07103 4.9 42.0 0.5 C A:ILE7088 4.9 52.3 1.0 CA A:VAL6916 5.0 56.5 1.0 O1 A:XDU7102 5.0 67.1 0.5 CG A:LEU6909 5.0 64.3 1.0

Fluorine binding site 5 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7103 b:60.8 occ:0.50 F1 A:XE07103 0.0 60.8 0.5 F2 A:XDU7102 0.3 61.8 0.5 C13 A:XE07103 1.3 60.3 0.5 C13 A:XDU7102 1.5 65.7 0.5 F2 A:XE07103 2.2 69.1 0.5 F3 A:XE07103 2.2 72.4 0.5 F3 A:XDU7102 2.2 71.7 0.5 C12 A:XE07103 2.3 52.2 0.5 C12 A:XDU7102 2.3 62.2 0.5 F1 A:XDU7102 2.4 72.7 0.5 C11 A:XDU7102 2.5 62.0 0.5 C11 A:XE07103 2.6 46.9 0.5 N2 A:XE07103 3.5 46.9 0.5 N2 A:XDU7102 3.6 60.5 0.5 CD1 A:ILE6866 3.6 42.8 1.0 C2 A:XDU7102 3.8 69.9 0.5 CG2 A:ILE7088 3.9 59.9 1.0 C2 A:XE07103 4.0 46.5 0.5 CG A:LEU6909 4.1 64.3 1.0 CD1 A:ILE7088 4.1 66.6 1.0 CD2 A:LEU6909 4.2 75.6 1.0 CG2 A:VAL6916 4.3 59.4 1.0 CB A:VAL6916 4.4 60.5 1.0 C3 A:XDU7102 4.5 77.8 0.5 CG1 A:ILE7088 4.6 54.5 1.0 C1 A:XE07103 4.6 45.9 0.5 C1 A:XDU7102 4.6 64.7 0.5 N1 A:XDU7102 4.7 64.0 0.5 C3 A:XE07103 4.8 49.9 0.5 N1 A:XE07103 4.8 45.6 0.5 CB A:LEU6909 4.8 55.9 1.0 CG1 A:ILE6866 4.8 41.4 1.0 CG1 A:VAL6894 4.8 42.8 1.0 CB A:ILE7088 4.9 55.1 1.0 CE1 A:PHE6868 5.0 51.5 1.0

Fluorine binding site 6 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F7103 b:69.1 occ:0.50 F2 A:XE07103 0.0 69.1 0.5 F3 A:XDU7102 0.3 71.7 0.5 C13 A:XE07103 1.3 60.3 0.5 C13 A:XDU7102 1.4 65.7 0.5 F2 A:XDU7102 2.1 61.8 0.5 F1 A:XE07103 2.2 60.8 0.5 F3 A:XE07103 2.2 72.4 0.5 C12 A:XE07103 2.3 52.2 0.5 C12 A:XDU7102 2.4 62.2 0.5 F1 A:XDU7102 2.4 72.7 0.5 N2 A:XE07103 3.0 46.9 0.5 C11 A:XDU7102 3.2 62.0 0.5 C11 A:XE07103 3.2 46.9 0.5 N2 A:XDU7102 3.2 60.5 0.5 CG2 A:THR6918 3.2 50.2 1.0 CD1 A:ILE6866 3.5 42.8 1.0 CB A:THR6918 3.6 52.4 1.0 CZ2 A:TRP6922 3.8 45.3 1.0 CD1 A:ILE7088 3.8 66.6 1.0 CG1 A:ILE7088 4.0 54.5 1.0 CE2 A:TRP6922 4.2 43.0 1.0 NE1 A:TRP6922 4.2 43.6 1.0 C1 A:XE07103 4.3 45.9 0.5 CE1 A:PHE6954 4.3 46.1 1.0 C1 A:XDU7102 4.3 64.7 0.5 C2 A:XE07103 4.4 46.5 0.5 C2 A:XDU7102 4.4 69.9 0.5 CZ A:PHE6954 4.4 43.9 1.0 CG2 A:ILE7088 4.4 59.9 1.0 OG1 A:THR6918 4.5 51.2 1.0 CH2 A:TRP6922 4.6 42.3 1.0 CB A:ILE7088 4.8 55.1 1.0 N A:THR6918 4.8 49.0 1.0 CG1 A:ILE6866 4.8 41.4 1.0 N1 A:XE07103 4.8 45.6 0.5 CA A:THR6918 4.8 51.5 1.0 N1 A:XDU7102 4.8 64.0 0.5 C A:HIS6917 5.0 55.6 1.0

Fluorine binding site 7 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F4404 b:117.9 occ:0.80 F3 B:XE04404 0.0 117.9 0.8 C13 B:XE04404 1.3 114.6 0.8 F2 B:XE04404 2.2 118.8 0.8 F1 B:XE04404 2.2 119.8 0.8 C12 B:XE04404 2.3 106.0 0.8 N2 B:XE04404 3.0 90.7 0.8 C11 B:XE04404 3.3 96.6 0.8 O B:THR4355 3.6 69.0 1.0 CB B:THR4355 3.8 73.2 1.0 C1 B:XE04404 4.2 95.2 0.8 CA B:THR4355 4.3 68.5 1.0 CG2 B:THR4355 4.3 69.3 1.0 C B:THR4355 4.3 67.5 1.0 C2 B:XE04404 4.5 95.5 0.8 OG1 B:THR4355 4.8 76.7 1.0 N1 B:XE04404 4.8 90.8 0.8

Fluorine binding site 8 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F4404 b:119.8 occ:0.80 F1 B:XE04404 0.0 119.8 0.8 C13 B:XE04404 1.3 114.6 0.8 F2 B:XE04404 2.2 118.8 0.8 F3 B:XE04404 2.2 117.9 0.8 C12 B:XE04404 2.3 106.0 0.8 N2 B:XE04404 2.8 90.7 0.8 C11 B:XE04404 3.5 96.6 0.8 C1 B:XE04404 4.1 95.2 0.8 C2 B:XE04404 4.6 95.5 0.8 N1 B:XE04404 4.8 90.8 0.8 O B:XE04404 4.9 90.1 0.8

Fluorine binding site 9 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F4404 b:118.8 occ:0.80 F2 B:XE04404 0.0 118.8 0.8 C13 B:XE04404 1.3 114.6 0.8 F1 B:XE04404 2.2 119.8 0.8 F3 B:XE04404 2.2 117.9 0.8 C12 B:XE04404 2.3 106.0 0.8 C11 B:XE04404 2.7 96.6 0.8 N2 B:XE04404 3.6 90.7 0.8 C2 B:XE04404 4.1 95.5 0.8 O B:THR4355 4.4 69.0 1.0 C1 B:XE04404 4.7 95.2 0.8 N1 B:XE04404 4.9 90.8 0.8

Fluorine binding site 10 out of 12 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F4405 b:107.4 occ:0.70 F3 B:XE04405 0.0 107.4 0.7 C13 B:XE04405 1.3 119.7 0.7 F1 B:XE04405 2.2 117.3 0.7 F2 B:XE04405 2.2 122.4 0.7 C12 B:XE04405 2.3 122.3 0.7 N2 B:XE04405 2.7 126.0 0.7 C11 B:XE04405 3.6 123.3 0.7 C1 B:XE04405 4.0 123.1 0.7 C2 B:XE04405 4.7 120.4 0.7 CG2 B:ILE4334 4.8 106.1 1.0 N1 B:XE04405 4.8 123.8 0.7 O B:XE04405 4.8 121.4 0.7

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