Fluorine in PDB 5vrj: 2009 H1N1 Pa Endonuclease in Complex with Ro-7 and Magnesium

The structure of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 and Magnesium, PDB code: 5vrj 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)	38.91 / 2.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.924, 90.924, 133.913, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.7

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

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the 2009 H1N1 Pa Endonuclease in Complex with Ro-7 and Magnesium (pdb code 5vrj). 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 and Magnesium, PDB code: 5vrj:
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 and Magnesium


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 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:84.1 occ:1.00 F27 A:R07204 0.0 84.1 1.0 C22 A:R07204 1.4 77.8 1.0 F28 A:R07204 2.2 74.4 1.0 F29 A:R07204 2.2 78.7 1.0 C20 A:R07204 2.4 72.1 1.0 C23 A:R07204 2.9 70.3 1.0 N13 A:R07204 3.6 67.5 1.0 CD1 A:LEU106 3.8 75.8 1.0 OH A:TYR24 3.8 91.0 1.0 CB A:LEU106 3.9 73.2 1.0 CG A:LEU106 4.3 74.2 1.0 O18 A:R07204 4.4 64.3 1.0 C14 A:R07204 4.5 64.6 1.0 C10 A:R07204 4.6 70.3 1.0 CZ A:TYR24 4.7 83.9 1.0

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


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 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:74.4 occ:1.00 F28 A:R07204 0.0 74.4 1.0 C22 A:R07204 1.4 77.8 1.0 F27 A:R07204 2.2 84.1 1.0 F29 A:R07204 2.2 78.7 1.0 C20 A:R07204 2.4 72.1 1.0 N13 A:R07204 2.8 67.5 1.0 O18 A:R07204 3.2 64.3 1.0 C14 A:R07204 3.2 64.6 1.0 C23 A:R07204 3.7 70.3 1.0 CB A:LEU106 3.8 73.2 1.0 C10 A:R07204 3.8 70.3 1.0 O A:LEU106 3.8 69.5 1.0 O A:HOH302 4.0 51.6 1.0 C07 A:R07204 4.3 60.3 1.0 O A:HOH301 4.5 57.1 1.0 N A:LEU106 4.5 77.7 1.0 MG A:MG203 4.5 63.1 1.0 CA A:LEU106 4.5 73.2 1.0 C A:LEU106 4.6 68.7 1.0 O15 A:R07204 4.8 59.0 1.0 CD1 A:LEU106 4.9 75.8 1.0 N09 A:R07204 4.9 70.5 1.0 CG A:LEU106 4.9 74.2 1.0 C08 A:R07204 5.0 62.3 1.0

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


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 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:78.7 occ:1.00 F29 A:R07204 0.0 78.7 1.0 C22 A:R07204 1.4 77.8 1.0 F27 A:R07204 2.2 84.1 1.0 F28 A:R07204 2.2 74.4 1.0 C20 A:R07204 2.4 72.1 1.0 C23 A:R07204 2.8 70.3 1.0 N13 A:R07204 2.8 67.5 1.0 C10 A:R07204 3.0 70.3 1.0 C14 A:R07204 3.9 64.6 1.0 N09 A:R07204 4.3 70.5 1.0 O18 A:R07204 4.4 64.3 1.0 C07 A:R07204 4.9 60.3 1.0 OH A:TYR24 4.9 91.0 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