Fluorine in PDB 5vpt: 2009 H1N1 Pa Endonuclease in Complex with Ro-7

The structure of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vpt 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)	38.50 / 2.10
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.881, 89.881, 133.731, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22

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

Fluorine binding site 1 out of 3 in the 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 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:65.5 occ:1.00 F27 A:R07204 0.0 65.5 1.0 C22 A:R07204 1.4 70.1 1.0 F29 A:R07204 2.2 66.6 1.0 F28 A:R07204 2.2 78.6 1.0 C20 A:R07204 2.4 66.1 1.0 C23 A:R07204 2.8 66.5 1.0 N13 A:R07204 2.8 60.6 1.0 C10 A:R07204 3.1 63.4 1.0 C14 A:R07204 3.8 54.2 1.0 O18 A:R07204 4.3 55.0 1.0 N09 A:R07204 4.4 63.5 1.0 C07 A:R07204 4.8 53.3 1.0 OH A:TYR24 4.9 77.3 1.0

Fluorine binding site 2 out of 3 in the 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 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:78.6 occ:1.00 F28 A:R07204 0.0 78.6 1.0 C22 A:R07204 1.4 70.1 1.0 F29 A:R07204 2.2 66.6 1.0 F27 A:R07204 2.2 65.5 1.0 C20 A:R07204 2.3 66.1 1.0 C23 A:R07204 2.8 66.5 1.0 N13 A:R07204 3.6 60.6 1.0 CD2 A:LEU106 3.7 64.7 1.0 OH A:TYR24 3.8 77.3 1.0 CB A:LEU106 3.9 61.8 1.0 O18 A:R07204 4.3 55.0 1.0 C14 A:R07204 4.4 54.2 1.0 CG A:LEU106 4.4 63.5 1.0 C10 A:R07204 4.6 63.4 1.0 CZ A:TYR24 4.7 72.2 1.0

Fluorine binding site 3 out of 3 in the 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 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:66.6 occ:1.00 F29 A:R07204 0.0 66.6 1.0 C22 A:R07204 1.4 70.1 1.0 F27 A:R07204 2.2 65.5 1.0 F28 A:R07204 2.2 78.6 1.0 C20 A:R07204 2.4 66.1 1.0 N13 A:R07204 2.8 60.6 1.0 O18 A:R07204 3.0 55.0 1.0 C14 A:R07204 3.1 54.2 1.0 C23 A:R07204 3.7 66.5 1.0 CB A:LEU106 3.8 61.8 1.0 O A:LEU106 3.8 63.2 1.0 C10 A:R07204 3.9 63.4 1.0 O A:HOH303 4.1 46.5 1.0 C07 A:R07204 4.2 53.3 1.0 MN A:MN202 4.4 59.6 1.0 O A:HOH301 4.4 46.5 1.0 C A:LEU106 4.5 62.5 1.0 CA A:LEU106 4.5 62.4 1.0 CD2 A:LEU106 4.6 64.7 1.0 N A:LEU106 4.6 67.2 1.0 O15 A:R07204 4.7 49.1 1.0 CG A:LEU106 4.7 63.5 1.0 C08 A:R07204 4.9 53.1 1.0 N09 A:R07204 5.0 63.5 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