Fluorine in PDB 7kaf: The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid, PDB code: 7kaf was solved by M.G.Cuypers, G.Kumar, J.Slavish, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.06 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.824, 89.824, 133.773, 90, 90, 90
R / Rfree (%)	19.2 / 23.5

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid (pdb code 7kaf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid, PDB code: 7kaf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:68.4 occ:1.00 F2 A:E4Z201 0.0 68.4 1.0 C23 A:E4Z201 1.4 71.2 1.0 C22 A:E4Z201 2.4 58.2 1.0 C24 A:E4Z201 2.4 58.6 1.0 H11 A:E4Z201 2.6 70.0 1.0 F1 A:E4Z201 2.8 71.4 1.0 CB A:TYR24 3.2 74.9 1.0 CG A:GLU26 3.3 79.0 1.0 CA A:MET21 3.3 46.5 1.0 O A:MET21 3.4 80.4 1.0 C13 A:E4Z201 3.7 60.5 1.0 C21 A:E4Z201 3.7 62.0 1.0 CB A:GLU26 3.7 69.1 1.0 C A:MET21 3.8 71.4 1.0 CG A:TYR24 3.9 71.1 1.0 O A:ALA20 3.9 57.1 1.0 CD2 A:TYR24 4.0 64.3 1.0 CB A:MET21 4.0 46.3 1.0 CG A:MET21 4.1 45.4 1.0 C12 A:E4Z201 4.2 58.8 1.0 N A:MET21 4.2 50.1 1.0 CA A:TYR24 4.3 63.4 1.0 H10 A:E4Z201 4.4 74.6 1.0 C A:ALA20 4.4 55.3 1.0 N A:TYR24 4.5 71.8 1.0 CD A:GLU26 4.6 86.0 1.0 C A:TYR24 4.6 83.8 1.0 H4 A:E4Z201 4.7 67.0 1.0 N A:GLU26 4.7 65.4 1.0 O A:TYR24 4.7 83.6 1.0 CD A:LYS34 4.7 74.9 1.0 C14 A:E4Z201 4.8 55.8 1.0 CA A:GLU26 4.8 69.1 1.0 OE2 A:GLU26 5.0 100.3 1.0 CD1 A:TYR24 5.0 68.2 1.0

Fluorine binding site 2 out of 2 in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:71.4 occ:1.00 F1 A:E4Z201 0.0 71.4 1.0 C24 A:E4Z201 1.4 58.6 1.0 H4 A:E4Z201 2.2 67.0 1.0 C23 A:E4Z201 2.4 71.2 1.0 C13 A:E4Z201 2.4 60.5 1.0 C14 A:E4Z201 2.7 55.8 1.0 F2 A:E4Z201 2.8 68.4 1.0 CD A:LYS34 3.3 74.9 1.0 H5 A:E4Z201 3.4 67.0 1.0 C22 A:E4Z201 3.7 58.2 1.0 C12 A:E4Z201 3.7 58.8 1.0 CG A:GLU26 3.7 79.0 1.0 S3 A:E4Z201 3.9 53.9 1.0 NZ A:LYS34 3.9 83.0 1.0 CE A:LYS34 4.1 88.3 1.0 OE2 A:GLU26 4.1 100.3 1.0 CD A:GLU26 4.2 86.0 1.0 C21 A:E4Z201 4.2 62.0 1.0 H11 A:E4Z201 4.4 70.0 1.0 O A:HOH358 4.5 65.6 1.0 CG A:LYS34 4.5 71.7 1.0 CB A:TYR24 4.6 74.9 1.0 CB A:GLU26 4.8 69.1 1.0 H3 A:E4Z201 4.9 58.1 1.0

G.Kumar, M.Cuypers, R.R.Webby, T.R.Webb, S.W.White. Structural Insights Into the Substrate Specificity of the Endonuclease Activity of the Influenza Virus Cap-Snatching Mechanism. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33469660
DOI: 10.1093/NAR/GKAA1294