Fluorine in PDB 8t5v: Influenza Pa-N Endonuclease A36V Mutant with Baloxavir

The structure of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir, PDB code: 8t5v was solved by A.J.Kohlbrand, S.M.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.71 / 1.79
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.724, 74.724, 121.619, 90, 90, 120
R / Rfree (%)	23.2 / 28.4

The structure of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir (pdb code 8t5v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir, PDB code: 8t5v:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:54.6 occ:1.00 F2 A:E4Z303 0.0 54.6 1.0 C23 A:E4Z303 1.4 50.4 1.0 C24 A:E4Z303 2.4 50.5 1.0 C22 A:E4Z303 2.4 51.5 1.0 H11 A:E4Z303 2.7 62.4 1.0 F1 A:E4Z303 2.7 55.3 1.0 CG A:GLU26 3.2 61.8 1.0 CB A:TYR24 3.4 65.6 1.0 CA A:MET21 3.4 56.1 1.0 CB A:GLU26 3.6 60.1 1.0 C13 A:E4Z303 3.7 47.5 1.0 C21 A:E4Z303 3.7 49.0 1.0 O A:MET21 3.8 61.4 1.0 O A:ALA20 4.0 56.7 1.0 CG A:MET21 4.0 46.3 1.0 CG A:TYR24 4.1 67.3 1.0 C A:MET21 4.1 58.4 1.0 CB A:MET21 4.1 53.5 1.0 N A:MET21 4.1 53.7 1.0 C12 A:E4Z303 4.2 49.0 1.0 CD1 A:TYR24 4.3 63.6 1.0 CD1 A:ILE38 4.3 43.0 1.0 C A:ALA20 4.4 54.1 1.0 CA A:TYR24 4.4 65.0 1.0 CD A:GLU26 4.5 63.5 1.0 CD A:LYS34 4.5 47.4 1.0 H10 A:E4Z303 4.6 59.4 1.0 N A:TYR24 4.6 63.3 1.0 CE A:MET21 4.7 50.8 1.0 C A:TYR24 4.7 66.3 1.0 N A:GLU26 4.7 60.7 1.0 CA A:GLU26 4.8 58.7 1.0 H4 A:E4Z303 4.9 62.3 1.0 O A:TYR24 4.9 67.5 1.0 C14 A:E4Z303 4.9 51.5 1.0 OE1 A:GLU26 5.0 65.9 1.0

Fluorine binding site 2 out of 2 in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:55.3 occ:1.00 F1 A:E4Z303 0.0 55.3 1.0 C24 A:E4Z303 1.4 50.5 1.0 C23 A:E4Z303 2.4 50.4 1.0 H4 A:E4Z303 2.4 62.3 1.0 C13 A:E4Z303 2.4 47.5 1.0 F2 A:E4Z303 2.7 54.6 1.0 C14 A:E4Z303 2.9 51.5 1.0 CD A:LYS34 3.1 47.4 1.0 NZ A:LYS34 3.4 63.0 1.0 CG A:GLU26 3.6 61.8 1.0 C12 A:E4Z303 3.7 49.0 1.0 C22 A:E4Z303 3.7 51.5 1.0 H5 A:E4Z303 3.7 62.3 1.0 CE A:LYS34 3.8 54.9 1.0 S3 A:E4Z303 3.9 51.8 1.0 CD A:GLU26 4.1 63.5 1.0 C21 A:E4Z303 4.2 49.0 1.0 OE1 A:GLU26 4.2 65.9 1.0 CG A:LYS34 4.3 47.1 1.0 H11 A:E4Z303 4.6 62.4 1.0 CB A:TYR24 4.6 65.6 1.0 CB A:GLU26 4.7 60.1 1.0 OE2 A:GLU26 4.8 67.0 1.0 H3 A:E4Z303 4.9 61.0 1.0 CD1 A:ILE38 4.9 43.0 1.0

A.J.Kohlbrand, R.W.Stokes, B.Sankaran, S.M.Cohen. Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants. Biochemistry V. 63 264 2024.
ISSN: ISSN 0006-2960
PubMed: 38190441
DOI: 10.1021/ACS.BIOCHEM.3C00536