Fluorine in PDB 5vpx: I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7

The structure of I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vpx 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)	38.82 / 2.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.672, 90.672, 134.165, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.4

The structure of I38T 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 I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 (pdb code 5vpx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vpx:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the I38T 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 I38T 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:82.4 occ:1.00 F27 A:R07205 0.0 82.4 1.0 C22 A:R07205 1.4 79.5 1.0 F29 A:R07205 2.2 77.8 1.0 F28 A:R07205 2.2 79.6 1.0 C20 A:R07205 2.4 75.8 1.0 C23 A:R07205 2.9 73.0 1.0 OH A:TYR24 3.4 91.2 1.0 N13 A:R07205 3.6 71.9 1.0 CD1 A:LEU106 3.6 76.8 1.0 CB A:LEU106 3.9 70.2 1.0 CZ A:TYR24 4.1 88.2 1.0 CG A:LEU106 4.3 74.5 1.0 O18 A:R07205 4.3 70.7 1.0 C14 A:R07205 4.4 66.2 1.0 C10 A:R07205 4.6 73.6 1.0 CE2 A:TYR24 4.7 90.5 1.0 CE1 A:TYR24 4.7 77.9 1.0

Fluorine binding site 2 out of 3 in the I38T 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 I38T 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:79.6 occ:1.00 F28 A:R07205 0.0 79.6 1.0 C22 A:R07205 1.4 79.5 1.0 F29 A:R07205 2.2 77.8 1.0 F27 A:R07205 2.2 82.4 1.0 C20 A:R07205 2.4 75.8 1.0 N13 A:R07205 2.8 71.9 1.0 O18 A:R07205 3.1 70.7 1.0 C14 A:R07205 3.1 66.2 1.0 C23 A:R07205 3.7 73.0 1.0 CB A:LEU106 3.8 70.2 1.0 O A:LEU106 3.8 63.1 1.0 C10 A:R07205 3.8 73.6 1.0 O A:HOH302 4.0 46.8 1.0 C07 A:R07205 4.2 61.9 1.0 O A:HOH304 4.4 54.9 1.0 MN A:MN202 4.4 65.0 1.0 CA A:LEU106 4.5 71.2 1.0 N A:LEU106 4.5 78.6 1.0 C A:LEU106 4.6 67.5 1.0 CD1 A:LEU106 4.8 76.8 1.0 O15 A:R07205 4.8 61.2 1.0 CG A:LEU106 4.9 74.5 1.0 N09 A:R07205 4.9 72.2 1.0 C08 A:R07205 5.0 58.3 1.0

Fluorine binding site 3 out of 3 in the I38T 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 I38T 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:77.8 occ:1.00 F29 A:R07205 0.0 77.8 1.0 C22 A:R07205 1.4 79.5 1.0 F28 A:R07205 2.2 79.6 1.0 F27 A:R07205 2.2 82.4 1.0 C20 A:R07205 2.4 75.8 1.0 C23 A:R07205 2.8 73.0 1.0 N13 A:R07205 2.9 71.9 1.0 C10 A:R07205 3.1 73.6 1.0 C14 A:R07205 3.9 66.2 1.0 O18 A:R07205 4.4 70.7 1.0 N09 A:R07205 4.4 72.2 1.0 OH A:TYR24 4.6 91.2 1.0 CZ A:TYR24 4.7 88.2 1.0 CE2 A:TYR24 4.8 90.5 1.0 C07 A:R07205 4.9 61.9 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