Fluorine in PDB 4yyl: Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease

The structure of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease, PDB code: 4yyl was solved by S.Fudo, N.Yamamoto, M.Nukaga, T.Odagiri, M.Tashiro, S.Neya, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.27 / 1.91
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.766, 66.766, 126.251, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.4

The structure of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Fluorine atom in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease (pdb code 4yyl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease, PDB code: 4yyl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:56.9 occ:1.00 FAT A:4KN301 0.0 56.9 1.0 CAS A:4KN301 1.6 71.8 1.0 CAR A:4KN301 2.6 68.1 1.0 CAQ A:4KN301 2.6 88.3 1.0 N A:LEU106 3.2 33.6 1.0 NH1 A:ARG84 3.2 74.1 1.0 CA A:PHE105 3.7 41.1 1.0 CAP A:4KN301 3.8 89.4 1.0 C A:PHE105 3.9 37.1 1.0 CAO A:4KN301 3.9 88.7 1.0 CG A:LEU106 4.0 45.4 1.0 CB A:LEU106 4.0 38.3 1.0 CB A:PHE105 4.0 48.4 1.0 CA A:LEU106 4.2 35.7 1.0 CD2 A:PHE105 4.2 61.8 1.0 CZ A:ARG84 4.2 80.9 1.0 CZ2 A:TRP88 4.3 40.9 1.0 CD1 A:LEU106 4.3 43.6 1.0 NH2 A:ARG84 4.4 80.5 1.0 CAN A:4KN301 4.4 93.4 1.0 NE1 A:TRP88 4.5 40.1 1.0 CG A:PHE105 4.6 52.8 1.0 O A:LYS104 4.7 51.5 1.0 CE2 A:TRP88 4.8 38.3 1.0 N A:PHE105 5.0 40.0 1.0 O A:LEU106 5.0 36.2 1.0

Fluorine binding site 2 out of 3 in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:85.0 occ:1.00 FAT A:4KN302 0.0 85.0 1.0 CAS A:4KN302 1.4 67.6 1.0 CAR A:4KN302 2.4 72.7 1.0 CAQ A:4KN302 2.4 75.1 1.0 OE1 A:GLU26 3.2 68.6 1.0 CE A:LYS34 3.2 59.7 1.0 NZ A:LYS34 3.4 62.6 1.0 CAP A:4KN302 3.7 71.0 1.0 CAO A:4KN302 3.7 77.1 1.0 CD A:GLU26 3.9 68.7 1.0 OE2 A:GLU26 4.1 74.0 1.0 CD1 A:ILE38 4.2 40.6 1.0 CAN A:4KN302 4.2 69.0 1.0 CD A:LYS34 4.3 53.5 1.0 CB A:TYR24 4.3 55.6 1.0 CG A:TYR24 4.5 69.4 1.0 CD1 A:TYR24 4.7 64.5 1.0 CG2 A:THR20 5.0 46.9 1.0

Fluorine binding site 3 out of 3 in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:44.2 occ:1.00 FAT A:4KN303 0.0 44.2 1.0 CAS A:4KN303 1.4 46.3 1.0 CAQ A:4KN303 2.4 33.4 1.0 CAR A:4KN303 2.4 41.3 1.0 CE1 A:PHE150 3.3 29.0 1.0 N A:ARG124 3.6 34.0 1.0 CAP A:4KN303 3.7 37.1 1.0 CE2 A:PHE191 3.7 28.6 1.0 CAO A:4KN303 3.7 34.5 1.0 CD1 A:PHE150 3.7 33.0 1.0 OE1 A:GLU195 3.7 38.3 1.0 CB A:ARG124 3.8 35.1 1.0 C A:THR123 4.0 34.8 1.0 CZ A:PHE191 4.1 36.7 1.0 CAN A:4KN303 4.2 37.1 1.0 CZ A:PHE150 4.3 30.3 1.0 CA A:ARG124 4.3 31.2 1.0 CD2 A:PHE191 4.3 32.4 1.0 CA A:THR123 4.4 34.5 1.0 O A:HOH449 4.5 38.8 1.0 O A:THR123 4.5 28.0 1.0 CD A:GLU195 4.5 42.2 1.0 CB A:GLU195 4.8 37.5 1.0 CH2 A:TRP188 4.8 32.0 1.0 CA A:ARG192 4.9 30.3 1.0 CG A:PHE150 4.9 33.8 1.0 O A:PHE191 4.9 34.0 1.0

S.Fudo, N.Yamamoto, M.Nukaga, T.Odagiri, M.Tashiro, S.Neya, T.Hoshino. Structural and Computational Study on the Inhibitory Compounds For Endonuclease Activity of Influenza Virus Polymerase To Be Published.