Fluorine in PDB 8t5w: Influenza Pan Endonuclease I38T Mutant with Baloxavir

The structure of Influenza Pan Endonuclease I38T Mutant with Baloxavir, PDB code: 8t5w 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)	57.34 / 1.65
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.111, 75.111, 121.444, 90, 90, 120
R / Rfree (%)	20.2 / 23.4

The structure of Influenza Pan Endonuclease I38T Mutant with Baloxavir also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the Influenza Pan Endonuclease I38T Mutant with Baloxavir (pdb code 8t5w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Influenza Pan Endonuclease I38T Mutant with Baloxavir, PDB code: 8t5w:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Influenza Pan Endonuclease I38T 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 Pan Endonuclease I38T Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:38.4 occ:1.00 F2 A:E4Z303 0.0 38.4 1.0 C23 A:E4Z303 1.4 41.5 1.0 C24 A:E4Z303 2.3 38.1 1.0 C22 A:E4Z303 2.4 39.8 1.0 F1 A:E4Z303 2.7 42.7 1.0 H11 A:E4Z303 2.7 47.8 1.0 CB A:TYR24 3.2 53.2 1.0 CG A:GLU26 3.3 54.5 1.0 CA A:MET21 3.3 38.2 1.0 CG A:MET21 3.5 39.1 1.0 O A:TYR24 3.6 67.1 1.0 CB A:GLU26 3.6 52.4 1.0 C13 A:E4Z303 3.6 35.5 1.0 O A:MET21 3.7 44.8 1.0 C21 A:E4Z303 3.7 34.1 1.0 CB A:MET21 3.8 37.8 1.0 O A:ALA20 3.8 38.5 1.0 C A:MET21 4.0 42.2 1.0 C12 A:E4Z303 4.1 36.7 1.0 C A:TYR24 4.2 54.5 1.0 CA A:TYR24 4.2 55.9 1.0 N A:MET21 4.2 37.0 1.0 CG A:TYR24 4.3 59.6 1.0 C A:ALA20 4.4 37.8 1.0 N A:GLU26 4.6 46.8 1.0 H10 A:E4Z303 4.6 40.9 1.0 CD A:GLU26 4.6 60.4 1.0 H5 A:E4Z303 4.6 48.3 1.0 CA A:GLU26 4.7 50.4 1.0 N A:TYR24 4.7 54.8 1.0 C14 A:E4Z303 4.8 40.3 1.0 CD1 A:TYR24 4.8 57.0 1.0 CD A:LYS34 4.9 43.1 1.0 OE1 A:GLU26 5.0 62.3 1.0

Fluorine binding site 2 out of 4 in the Influenza Pan Endonuclease I38T 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 Pan Endonuclease I38T Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:42.7 occ:1.00 F1 A:E4Z303 0.0 42.7 1.0 C24 A:E4Z303 1.3 38.1 1.0 H5 A:E4Z303 2.1 48.3 1.0 C13 A:E4Z303 2.3 35.5 1.0 C23 A:E4Z303 2.4 41.5 1.0 C14 A:E4Z303 2.7 40.3 1.0 F2 A:E4Z303 2.7 38.4 1.0 CD A:LYS34 3.3 43.1 1.0 CG A:GLU26 3.4 54.5 1.0 H4 A:E4Z303 3.4 48.3 1.0 NZ A:LYS34 3.6 51.1 1.0 C12 A:E4Z303 3.6 36.7 1.0 C22 A:E4Z303 3.7 39.8 1.0 OE1 A:GLU26 3.7 62.3 1.0 CD A:GLU26 3.9 60.4 1.0 CE A:LYS34 3.9 43.6 1.0 S3 A:E4Z303 4.0 35.2 1.0 C21 A:E4Z303 4.1 34.1 1.0 CB A:GLU26 4.3 52.4 1.0 CG A:LYS34 4.4 34.4 1.0 H12 A:E4Z303 4.5 47.6 1.0 H11 A:E4Z303 4.5 47.8 1.0 C11 A:E4Z303 4.7 39.7 1.0 O A:TYR24 4.8 67.1 1.0 CB A:TYR24 4.9 53.2 1.0 OE2 A:GLU26 5.0 67.8 1.0

Fluorine binding site 3 out of 4 in the Influenza Pan Endonuclease I38T Mutant with Baloxavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Influenza Pan Endonuclease I38T Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:52.5 occ:1.00 F2 A:E4Z304 0.0 52.5 1.0 C23 A:E4Z304 1.4 45.4 1.0 C24 A:E4Z304 2.4 49.7 1.0 C22 A:E4Z304 2.4 49.9 1.0 F1 A:E4Z304 2.7 54.2 1.0 H11 A:E4Z304 2.7 59.8 1.0 OE2 A:GLU43 3.2 36.3 1.0 O A:HOH437 3.2 40.0 1.0 CD A:GLU43 3.2 34.9 1.0 CG A:GLU43 3.3 28.4 1.0 O A:HOH403 3.5 43.5 1.0 C13 A:E4Z304 3.6 47.6 1.0 C21 A:E4Z304 3.7 54.5 1.0 OE1 A:GLU43 3.9 35.8 1.0 O A:HOH414 3.9 40.5 1.0 CG1 A:ILE13 4.0 35.8 1.0 C12 A:E4Z304 4.2 52.7 1.0 CB A:ASN10 4.3 46.5 1.0 CD1 A:ILE13 4.3 38.7 1.0 CB A:GLU43 4.3 27.3 1.0 H10 A:E4Z304 4.6 65.3 1.0 H4 A:E4Z304 4.7 56.9 1.0 ND2 A:ASN10 4.8 52.8 1.0 CA A:GLU43 4.8 26.8 1.0 C14 A:E4Z304 4.8 47.5 1.0

Fluorine binding site 4 out of 4 in the Influenza Pan Endonuclease I38T Mutant with Baloxavir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Influenza Pan Endonuclease I38T Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:54.2 occ:1.00 F1 A:E4Z304 0.0 54.2 1.0 C24 A:E4Z304 1.4 49.7 1.0 H4 A:E4Z304 2.2 56.9 1.0 C23 A:E4Z304 2.4 45.4 1.0 C13 A:E4Z304 2.4 47.6 1.0 F2 A:E4Z304 2.7 52.5 1.0 C14 A:E4Z304 2.8 47.5 1.0 CG1 A:ILE13 2.9 35.8 1.0 CB A:ASN10 3.1 46.5 1.0 CG A:ASN10 3.3 44.2 1.0 ND2 A:ASN10 3.4 52.8 1.0 CD1 A:ILE13 3.4 38.7 1.0 H5 A:E4Z304 3.5 56.9 1.0 C12 A:E4Z304 3.7 52.7 1.0 C22 A:E4Z304 3.7 49.9 1.0 OD1 A:ASN10 4.0 50.5 1.0 S3 A:E4Z304 4.2 42.6 1.0 C21 A:E4Z304 4.2 54.5 1.0 CB A:ILE13 4.2 37.1 1.0 O A:HOH437 4.4 40.0 1.0 N A:ILE13 4.4 35.9 1.0 CA A:ASN10 4.5 41.5 1.0 H11 A:E4Z304 4.6 59.8 1.0 CD2 A:PHE46 4.8 36.6 1.0 CA A:ILE13 4.8 34.3 1.0 CB A:MET12 4.9 45.2 1.0 O A:HOH469 4.9 55.3 1.0 H12 A:E4Z304 4.9 65.3 1.0 C11 A:E4Z304 4.9 54.5 1.0 N A:ASN10 5.0 40.6 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