Fluorine in PDB 5vqn: E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7

The structure of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vqn was solved by G.Kumar, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.47 / 2.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.848, 89.848, 133.261, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 (pdb code 5vqn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vqn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F205 b:72.7 occ:1.00 F27 A:R07205 0.0 72.7 1.0 C22 A:R07205 1.4 64.1 1.0 F29 A:R07205 2.2 62.8 1.0 F28 A:R07205 2.2 62.3 1.0 C20 A:R07205 2.4 56.8 1.0 HD12 A:LEU106 2.5 80.9 1.0 H6 A:R07205 2.6 68.3 1.0 H9 A:R07205 2.6 72.5 1.0 C23 A:R07205 2.9 60.2 1.0 HB2 A:LEU106 3.1 63.5 1.0 H8 A:R07205 3.1 72.5 1.0 CD1 A:LEU106 3.4 67.3 1.0 N13 A:R07205 3.6 62.5 1.0 HH A:TYR24 3.6 0.9 1.0 HD13 A:LEU106 3.7 80.9 1.0 OH A:TYR24 3.7 90.6 1.0 H7 A:R07205 3.7 72.5 1.0 CB A:LEU106 3.9 52.8 1.0 HD11 A:LEU106 4.0 80.9 1.0 HB3 A:LEU106 4.1 63.5 1.0 CG A:LEU106 4.1 62.4 1.0 HG A:LEU106 4.2 75.1 1.0 O18 A:R07205 4.3 58.7 1.0 C14 A:R07205 4.4 55.3 1.0 H A:LEU106 4.4 78.0 1.0 H4 A:R07205 4.5 66.8 1.0 C10 A:R07205 4.6 55.5 1.0 CZ A:TYR24 4.6 80.8 1.0 H3 A:R07205 4.6 66.8 1.0 HG3 A:ARG84 4.8 98.2 1.0

Fluorine binding site 2 out of 3 in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F205 b:62.3 occ:1.00 F28 A:R07205 0.0 62.3 1.0 C22 A:R07205 1.4 64.1 1.0 F29 A:R07205 2.2 62.8 1.0 F27 A:R07205 2.2 72.7 1.0 C20 A:R07205 2.4 56.8 1.0 H6 A:R07205 2.6 68.3 1.0 N13 A:R07205 2.7 62.5 1.0 HB2 A:LEU106 2.8 63.5 1.0 O18 A:R07205 3.0 58.7 1.0 C14 A:R07205 3.1 55.3 1.0 H3 A:R07205 3.6 66.8 1.0 CB A:LEU106 3.6 52.8 1.0 HB3 A:LEU106 3.7 63.5 1.0 C23 A:R07205 3.7 60.2 1.0 C10 A:R07205 3.8 55.5 1.0 HD12 A:LEU106 3.8 80.9 1.0 O A:LEU106 3.8 64.7 1.0 H20 A:R07205 3.9 66.0 1.0 H A:LEU106 3.9 78.0 1.0 H8 A:R07205 3.9 72.5 1.0 O A:HOH301 3.9 59.8 1.0 H9 A:R07205 4.0 72.5 1.0 C07 A:R07205 4.1 53.1 1.0 H4 A:R07205 4.2 66.8 1.0 O A:HOH310 4.3 48.5 1.0 MN A:MN202 4.4 53.5 1.0 N A:LEU106 4.4 64.9 1.0 CA A:LEU106 4.4 59.8 1.0 H7 A:R07205 4.4 72.5 1.0 CD1 A:LEU106 4.5 67.3 1.0 HD13 A:LEU106 4.5 80.9 1.0 C A:LEU106 4.5 56.1 1.0 HB3 A:PHE105 4.6 0.6 1.0 O15 A:R07205 4.6 54.8 1.0 CG A:LEU106 4.6 62.4 1.0 C08 A:R07205 4.8 45.0 1.0 HG A:LEU106 4.9 75.1 1.0 N09 A:R07205 4.9 61.5 1.0 N06 A:R07205 5.0 58.2 1.0

Fluorine binding site 3 out of 3 in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F205 b:62.8 occ:1.00 F29 A:R07205 0.0 62.8 1.0 C22 A:R07205 1.4 64.1 1.0 F28 A:R07205 2.2 62.3 1.0 F27 A:R07205 2.2 72.7 1.0 C20 A:R07205 2.4 56.8 1.0 H8 A:R07205 2.5 72.5 1.0 H3 A:R07205 2.7 66.8 1.0 N13 A:R07205 2.8 62.5 1.0 C23 A:R07205 2.8 60.2 1.0 H4 A:R07205 2.9 66.8 1.0 C10 A:R07205 3.0 55.5 1.0 H6 A:R07205 3.2 68.3 1.0 H9 A:R07205 3.2 72.5 1.0 H7 A:R07205 3.7 72.5 1.0 C14 A:R07205 3.8 55.3 1.0 N09 A:R07205 4.3 61.5 1.0 O18 A:R07205 4.3 58.7 1.0 HB2 A:LEU106 4.4 63.5 1.0 HD12 A:LEU106 4.6 80.9 1.0 HH A:TYR24 4.7 0.9 1.0 C07 A:R07205 4.7 53.1 1.0 OH A:TYR24 4.8 90.6 1.0 H5 A:R07205 4.9 66.2 1.0 N06 A:R07205 5.0 58.2 1.0

J.C.Jones, G.Kumar, S.Barman, I.Najera, S.W.White, R.J.Webby, E.A.Govorkova. Identification of the I38T Pa Substitution As A Resistance Marker For Next-Generation Influenza Virus Endonuclease Inhibitors. Mbio V. 9 2018.
ISSN: ESSN 2150-7511
PubMed: 29691337
DOI: 10.1128/MBIO.00430-18