Fluorine in PDB 6euy: Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor

The structure of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor, PDB code: 6euy was solved by S.Cusack, S.Gaudon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.03 / 3.00
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	49.461, 112.322, 201.088, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.3

The binding sites of Fluorine atom in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor (pdb code 6euy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor, PDB code: 6euy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:75.8 occ:1.00 F23 A:BYB601 0.0 75.8 1.0 C1 A:BYB601 1.3 80.1 1.0 C2 A:BYB601 2.4 95.5 1.0 C4 A:BYB601 2.4 78.7 1.0 NE2 A:GLN406 3.3 0.1 1.0 CE A:MET431 3.3 0.6 1.0 CD A:GLN406 3.5 0.9 1.0 N3 A:BYB601 3.6 0.1 1.0 O A:PHE404 3.6 93.9 1.0 C5 A:BYB601 3.6 83.1 1.0 CG A:GLN406 3.9 0.5 1.0 CD1 A:PHE404 4.0 99.6 1.0 OE1 A:GLN406 4.0 0.3 1.0 C28 A:BYB601 4.0 53.0 1.0 CE1 A:PHE404 4.0 99.5 1.0 C6 A:BYB601 4.1 91.8 1.0 SD A:MET431 4.1 0.1 1.0 CD2 A:HIS357 4.4 0.4 1.0 C A:PHE404 4.5 92.3 1.0 O A:ARG355 4.6 0.3 1.0 CG A:MET431 4.6 0.5 1.0 CA A:PHE404 4.6 91.6 1.0 CG A:PHE404 4.7 98.0 1.0 C29 A:BYB601 4.7 60.8 1.0 CZ A:PHE404 4.8 97.0 1.0 NE2 A:HIS357 4.9 0.3 1.0 C18 A:BYB601 5.0 55.8 1.0 C9 A:BYB601 5.0 86.9 1.0

Fluorine binding site 2 out of 6 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:89.4 occ:1.00 F24 A:BYB601 0.0 89.4 1.0 C13 A:BYB601 1.4 87.0 1.0 C14 A:BYB601 2.4 93.1 1.0 C12 A:BYB601 2.4 79.0 1.0 N16 A:BYB601 2.8 63.2 1.0 CB A:ASN510 3.1 0.1 1.0 CD2 A:LEU512 3.4 91.9 1.0 O A:VAL511 3.5 73.7 1.0 CB A:PHE323 3.5 93.7 1.0 CG A:PHE323 3.6 0.0 1.0 N15 A:BYB601 3.6 94.5 1.0 N11 A:BYB601 3.6 86.6 1.0 C A:VAL511 3.8 71.6 1.0 C A:ASN510 3.9 90.5 1.0 CD1 A:PHE323 3.9 0.1 1.0 O A:ASN510 4.0 89.9 1.0 C10 A:BYB601 4.0 89.7 1.0 CD2 A:PHE323 4.1 0.5 1.0 CA A:ASN510 4.1 98.2 1.0 N A:VAL511 4.2 80.5 1.0 CG A:ASN510 4.2 0.1 1.0 N A:LEU512 4.2 72.5 1.0 C17 A:BYB601 4.2 57.5 1.0 CA A:LEU512 4.2 75.6 1.0 OD2 A:ASP506 4.4 0.3 1.0 CG A:LEU512 4.4 84.8 1.0 CE1 A:PHE323 4.6 0.3 1.0 CA A:VAL511 4.7 74.7 1.0 CE2 A:PHE323 4.8 0.1 1.0 ND2 A:ASN510 4.8 0.7 1.0 C22 A:BYB601 4.8 65.5 1.0 OD1 A:ASN510 4.8 0.4 1.0 CB A:LEU512 4.9 76.9 1.0 CZ A:PHE323 5.0 0.5 1.0 CA A:PHE323 5.0 84.3 1.0

Fluorine binding site 3 out of 6 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:0.5 occ:1.00 F23 B:BYB601 0.0 0.5 1.0 C1 B:BYB601 1.4 89.0 1.0 C2 B:BYB601 2.4 78.9 1.0 C4 B:BYB601 2.4 71.3 1.0 NE2 B:GLN406 3.2 83.5 1.0 CE B:MET431 3.3 93.5 1.0 CD B:GLN406 3.5 87.9 1.0 N3 B:BYB601 3.6 80.8 1.0 C5 B:BYB601 3.6 75.0 1.0 O B:PHE404 3.9 89.3 1.0 CG B:GLN406 3.9 92.0 1.0 SD B:MET431 3.9 90.8 1.0 CD2 B:HIS357 4.0 0.9 1.0 OE1 B:GLN406 4.1 89.9 1.0 C28 B:BYB601 4.1 66.2 1.0 C6 B:BYB601 4.1 85.5 1.0 C29 B:BYB601 4.2 62.4 1.0 CD1 B:PHE404 4.3 87.3 1.0 CG B:MET431 4.3 92.4 1.0 CE1 B:PHE404 4.3 90.9 1.0 O B:ARG355 4.4 0.8 1.0 NE2 B:HIS357 4.4 0.3 1.0 O27 B:BYB601 4.6 0.6 1.0 C B:PHE404 4.8 92.3 1.0 CG B:HIS357 4.8 0.5 1.0 CA B:PHE404 4.9 91.3 1.0 CG B:PHE404 5.0 84.7 1.0

Fluorine binding site 4 out of 6 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:0.7 occ:1.00 F24 B:BYB601 0.0 0.7 1.0 C13 B:BYB601 1.3 97.0 1.0 C14 B:BYB601 2.4 88.0 1.0 C12 B:BYB601 2.4 91.4 1.0 N16 B:BYB601 2.8 80.8 1.0 O B:VAL511 3.1 77.5 1.0 CB B:ASN510 3.3 89.8 1.0 CB B:PHE323 3.3 98.2 1.0 CG B:PHE323 3.3 93.3 1.0 N15 B:BYB601 3.6 82.5 1.0 N11 B:BYB601 3.6 91.8 1.0 CD2 B:LEU512 3.6 95.5 1.0 C B:VAL511 3.6 76.5 1.0 CD1 B:PHE323 3.7 85.4 1.0 CD2 B:PHE323 3.8 92.3 1.0 C B:ASN510 3.9 71.7 1.0 C10 B:BYB601 4.0 85.2 1.0 N B:VAL511 4.0 73.8 1.0 O B:ASN510 4.1 70.9 1.0 N B:LEU512 4.1 83.6 1.0 CA B:LEU512 4.1 86.6 1.0 CA B:ASN510 4.2 77.3 1.0 C17 B:BYB601 4.2 75.7 1.0 CG B:ASN510 4.3 0.2 1.0 CE1 B:PHE323 4.5 81.0 1.0 CE2 B:PHE323 4.5 88.1 1.0 CA B:VAL511 4.5 74.2 1.0 CG B:LEU512 4.6 92.8 1.0 OD2 B:ASP506 4.7 0.1 1.0 CA B:PHE323 4.8 96.9 1.0 CZ B:PHE323 4.8 82.2 1.0 OD1 B:ASN510 4.8 0.3 1.0 CB B:LEU512 4.8 87.4 1.0 C18 B:BYB601 5.0 69.7 1.0 C22 B:BYB601 5.0 84.1 1.0

Fluorine binding site 5 out of 6 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:82.7 occ:1.00 F23 C:BYB601 0.0 82.7 1.0 C1 C:BYB601 1.3 79.9 1.0 C2 C:BYB601 2.4 84.4 1.0 C4 C:BYB601 2.4 73.3 1.0 CE C:MET431 3.2 91.0 1.0 NE2 C:GLN406 3.4 94.3 1.0 N3 C:BYB601 3.6 82.5 1.0 C5 C:BYB601 3.6 74.8 1.0 CD C:GLN406 3.6 97.5 1.0 O C:PHE404 3.7 90.6 1.0 C28 C:BYB601 3.8 64.2 1.0 CG C:GLN406 4.0 99.5 1.0 SD C:MET431 4.0 89.4 1.0 C6 C:BYB601 4.1 74.2 1.0 CD1 C:PHE404 4.1 81.2 1.0 OE1 C:GLN406 4.2 99.7 1.0 CE1 C:PHE404 4.3 81.8 1.0 CG C:MET431 4.3 90.0 1.0 CD2 C:HIS357 4.4 0.8 1.0 C C:PHE404 4.6 88.4 1.0 C29 C:BYB601 4.6 59.3 1.0 CA C:PHE404 4.7 83.9 1.0 C18 C:BYB601 4.7 60.1 1.0 O C:ARG355 4.8 0.2 1.0 NE2 C:HIS357 4.8 0.6 1.0 CG C:PHE404 4.8 84.0 1.0 C9 C:BYB601 5.0 80.4 1.0

Fluorine binding site 6 out of 6 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindazole Cap-Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:97.5 occ:1.00 F24 C:BYB601 0.0 97.5 1.0 C13 C:BYB601 1.3 79.0 1.0 C14 C:BYB601 2.4 75.8 1.0 C12 C:BYB601 2.4 70.5 1.0 N16 C:BYB601 2.8 62.4 1.0 CB C:ASN510 3.2 93.5 1.0 O C:VAL511 3.3 76.4 1.0 CB C:PHE323 3.4 90.5 1.0 CG C:PHE323 3.4 84.6 1.0 CD2 C:LEU512 3.5 73.9 1.0 N15 C:BYB601 3.6 78.3 1.0 N11 C:BYB601 3.6 76.7 1.0 C C:VAL511 3.7 78.5 1.0 CD1 C:PHE323 3.8 85.0 1.0 C C:ASN510 3.9 91.3 1.0 CD2 C:PHE323 3.9 81.3 1.0 O C:ASN510 4.0 0.2 1.0 C10 C:BYB601 4.0 80.0 1.0 N C:LEU512 4.1 70.9 1.0 N C:VAL511 4.1 86.4 1.0 CA C:LEU512 4.1 70.2 1.0 CA C:ASN510 4.2 87.0 1.0 C17 C:BYB601 4.2 61.4 1.0 CG C:ASN510 4.3 0.3 1.0 CG C:LEU512 4.5 69.2 1.0 CE1 C:PHE323 4.5 90.8 1.0 OD2 C:ASP506 4.5 94.8 1.0 CE2 C:PHE323 4.6 82.7 1.0 CA C:VAL511 4.6 82.1 1.0 CB C:LEU512 4.8 66.7 1.0 CZ C:PHE323 4.8 87.9 1.0 CA C:PHE323 4.9 87.0 1.0 ND2 C:ASN510 4.9 0.7 1.0 C22 C:BYB601 4.9 66.0 1.0 OD1 C:ASN510 4.9 0.0 1.0

A.Pflug, S.Gaudon, P.Resa-Infante, M.Lethier, S.Reich, W.M.Schulze, S.Cusack. Capped Rna Primer Binding to Influenza Polymerase and Implications For the Mechanism of Cap-Binding Inhibitors. Nucleic Acids Res. V. 46 956 2018.
ISSN: ESSN 1362-4962
PubMed: 29202182
DOI: 10.1093/NAR/GKX1210