Fluorine in PDB 6euv: Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)

The structure of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787), PDB code: 6euv was solved by S.Cusack, M.Lethier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.35 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.490, 80.320, 92.320, 89.54, 107.12, 99.11
R / Rfree (%)	24.3 / 28.2

The structure of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787) also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

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 Azaindole Cap-Binding Inhibitor (Vx-787) (pdb code 6euv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 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 Azaindole Cap-Binding Inhibitor (Vx-787), PDB code: 6euv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


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 Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:28.1 occ:1.00 F31 A:21G601 0.0 28.1 1.0 C14 A:21G601 1.3 29.8 1.0 C15 A:21G601 2.4 28.7 1.0 C13 A:21G601 2.4 30.4 1.0 N17 A:21G601 2.8 29.8 1.0 O A:VAL511 3.3 29.6 1.0 CG A:PHE323 3.3 30.4 1.0 CB A:PHE323 3.3 30.4 1.0 CD2 A:LEU512 3.4 32.2 1.0 CB A:ASN510 3.5 34.1 1.0 CD1 A:PHE323 3.6 29.6 1.0 N16 A:21G601 3.6 26.9 1.0 N12 A:21G601 3.6 29.8 1.0 C A:VAL511 3.7 32.4 1.0 CD2 A:PHE323 3.8 31.0 1.0 CA A:LEU512 3.8 35.3 1.0 N A:LEU512 3.9 34.0 1.0 C A:ASN510 4.0 32.5 1.0 C11 A:21G601 4.1 27.6 1.0 O A:ASN510 4.2 33.1 1.0 C18 A:21G601 4.2 31.8 1.0 CG A:LEU512 4.2 32.7 1.0 N A:VAL511 4.3 31.8 1.0 CE1 A:PHE323 4.3 29.8 1.0 CA A:ASN510 4.4 32.9 1.0 CE2 A:PHE323 4.5 31.5 1.0 CG A:ASN510 4.6 35.8 1.0 CB A:LEU512 4.6 34.6 1.0 CA A:VAL511 4.6 34.1 1.0 CZ A:PHE323 4.7 31.1 1.0 CA A:PHE323 4.8 31.2 1.0 OD2 A:ASP506 4.8 47.0 1.0 ND2 A:ASN510 4.9 33.4 1.0 C20 A:21G601 4.9 33.4 1.0 C25 A:21G601 4.9 33.9 1.0 C A:LEU512 5.0 35.0 1.0

Fluorine binding site 2 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


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 Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:27.2 occ:1.00 F32 A:21G601 0.0 27.2 1.0 C2 A:21G601 1.4 25.4 1.0 C1 A:21G601 2.4 25.2 1.0 C3 A:21G601 2.4 24.7 1.0 CE A:MET431 3.1 40.2 1.0 NE2 A:GLN406 3.3 44.1 1.0 O A:PHE404 3.5 29.4 1.0 N4 A:21G601 3.6 24.9 1.0 C6 A:21G601 3.7 25.1 1.0 CD A:GLN406 3.7 41.7 1.0 CD1 A:PHE404 3.8 31.4 1.0 C26 A:21G601 3.9 34.9 1.0 CG A:GLN406 3.9 40.7 1.0 SD A:MET431 4.0 42.7 1.0 CE1 A:PHE404 4.1 29.8 1.0 C5 A:21G601 4.1 24.9 1.0 CA A:PHE404 4.2 31.4 1.0 C A:PHE404 4.3 32.2 1.0 OE1 A:GLN406 4.3 43.7 1.0 CG A:PHE404 4.4 30.7 1.0 CG A:MET431 4.4 36.9 1.0 C27 A:21G601 4.6 35.3 1.0 CD2 A:HIS357 4.7 32.5 1.0 CZ A:PHE404 4.8 29.6 1.0 C25 A:21G601 4.9 33.9 1.0 CB A:PHE404 4.9 31.6 1.0

Fluorine binding site 3 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


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 Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:65.5 occ:0.50 F31 A:21G602 0.0 65.5 0.5 C14 A:21G602 1.3 70.0 0.5 C13 A:21G602 2.4 69.3 0.5 C15 A:21G602 2.4 70.4 0.5 N17 A:21G602 2.8 75.3 0.5 OE2 I:GLU282 2.9 69.3 1.0 CG I:GLU282 3.3 62.7 1.0 CD I:GLU282 3.4 69.8 1.0 N12 A:21G602 3.6 68.1 0.5 N16 A:21G602 3.6 66.1 0.5 N4 A:21G602 3.8 67.0 0.5 C11 A:21G602 4.0 64.5 0.5 C3 A:21G602 4.1 65.5 0.5 C18 A:21G602 4.3 78.4 0.5 OE1 I:GLU282 4.5 67.0 1.0 CB I:GLU282 4.6 58.5 1.0 C5 A:21G602 4.6 65.2 0.5 OG I:SER286 4.6 61.4 1.0 C20 A:21G602 4.9 78.3 0.5 C23 A:21G602 5.0 76.1 0.5

Fluorine binding site 4 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


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 Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:65.2 occ:0.50 F31 A:21G602 0.0 65.2 0.5 C14 A:21G602 1.3 64.6 0.5 C15 A:21G602 2.3 65.2 0.5 C13 A:21G602 2.4 67.6 0.5 N17 A:21G602 2.7 62.0 0.5 N12 A:21G602 3.6 69.2 0.5 N16 A:21G602 3.6 67.7 0.5 CG A:GLU282 3.6 59.5 1.0 OE2 A:GLU282 3.7 79.4 1.0 CD A:GLU282 3.8 69.8 1.0 N9 A:21G602 3.8 57.4 0.5 N4 A:21G602 3.9 57.0 0.5 C11 A:21G602 4.0 67.8 0.5 C18 A:21G602 4.1 59.8 0.5 C5 A:21G602 4.2 57.0 0.5 CB A:GLU282 4.5 54.2 1.0 OE1 A:GLU282 4.6 80.7 1.0 C20 A:21G602 4.7 59.5 0.5 C24 A:21G602 4.7 58.7 0.5 C25 A:21G602 4.9 58.7 0.5

Fluorine binding site 5 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


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 Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:56.2 occ:0.50 F32 A:21G602 0.0 56.2 0.5 C2 A:21G602 1.3 55.8 0.5 CD2 A:HIS285 2.0 60.1 0.5 C1 A:21G602 2.3 54.8 0.5 C3 A:21G602 2.4 56.7 0.5 NE2 A:HIS285 2.5 59.9 0.5 CG A:HIS285 2.9 61.8 0.5 O30 A:21G602 3.0 71.9 0.5 C1 A:21G602 3.1 65.0 0.5 F32 A:21G602 3.2 70.3 0.5 C2 A:21G602 3.3 65.5 0.5 O A:LEU281 3.5 49.9 1.0 CE1 A:HIS285 3.5 60.7 0.5 C6 A:21G602 3.6 56.2 0.5 N4 A:21G602 3.6 57.0 0.5 ND1 A:HIS285 3.7 62.2 0.5 CB A:HIS285 3.7 60.4 0.5 CB A:HIS285 3.7 55.0 0.5 C25 A:21G602 3.9 58.7 0.5 C6 A:21G602 4.0 65.9 0.5 C26 A:21G602 4.0 57.6 0.5 C28 A:21G602 4.0 75.5 0.5 C5 A:21G602 4.1 57.0 0.5 C A:LEU281 4.3 45.2 1.0 C3 A:21G602 4.3 65.5 0.5 CB A:LEU281 4.3 45.0 1.0 CG A:HIS285 4.3 53.8 0.5 C26 A:21G602 4.4 79.4 0.5 N16 A:21G602 4.4 67.7 0.5 CD2 A:LEU281 4.5 49.2 1.0 O29 A:21G602 4.6 74.1 0.5 C18 A:21G602 4.7 78.4 0.5 CA A:LEU281 4.7 44.1 1.0 C7 A:21G602 4.7 66.5 0.5 CD2 A:HIS285 4.8 51.4 0.5 C18 A:21G602 4.8 59.8 0.5 C5 A:21G602 4.8 65.2 0.5 CD2 I:HIS285 4.9 61.8 0.5 C25 A:21G602 4.9 79.5 0.5 C7 A:21G602 4.9 59.9 0.5 C11 A:21G602 5.0 67.8 0.5 N16 A:21G602 5.0 66.1 0.5 N4 A:21G602 5.0 67.0 0.5

Fluorine binding site 6 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


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 Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:70.3 occ:0.50 F32 A:21G602 0.0 70.3 0.5 C2 A:21G602 1.3 65.5 0.5 C3 A:21G602 2.4 65.5 0.5 C1 A:21G602 2.4 65.0 0.5 C1 A:21G602 2.5 54.8 0.5 C18 A:21G602 2.9 78.4 0.5 N16 A:21G602 3.0 66.1 0.5 C25 A:21G602 3.0 79.5 0.5 C2 A:21G602 3.2 55.8 0.5 F32 A:21G602 3.2 56.2 0.5 O I:LEU281 3.4 49.3 1.0 C6 A:21G602 3.4 56.2 0.5 O30 A:21G602 3.5 71.9 0.5 C26 A:21G602 3.6 79.4 0.5 N17 A:21G602 3.6 75.3 0.5 N4 A:21G602 3.6 67.0 0.5 C6 A:21G602 3.6 65.9 0.5 C15 A:21G602 3.6 70.4 0.5 C I:LEU281 3.6 47.8 1.0 CA I:GLU282 3.7 56.2 1.0 N I:GLU282 3.7 50.7 1.0 NE2 A:HIS285 3.8 59.9 0.5 C11 A:21G602 3.8 64.5 0.5 C7 A:21G602 4.0 59.9 0.5 C5 A:21G602 4.0 65.2 0.5 CE1 A:HIS285 4.1 60.7 0.5 C20 A:21G602 4.1 78.3 0.5 C28 A:21G602 4.1 75.5 0.5 CD2 I:HIS285 4.3 61.8 0.5 CD2 A:HIS285 4.3 60.1 0.5 CB I:LEU281 4.3 52.7 1.0 C3 A:21G602 4.4 56.7 0.5 CB I:GLU282 4.5 58.5 1.0 C24 A:21G602 4.5 77.0 0.5 CB I:HIS285 4.5 60.2 0.5 C5 A:21G602 4.6 57.0 0.5 CB I:HIS285 4.6 53.6 0.5 CA I:LEU281 4.6 49.0 1.0 CG I:HIS285 4.6 62.5 0.5 ND1 I:HIS285 4.7 51.5 0.5 ND1 A:HIS285 4.7 62.2 0.5 CG I:HIS285 4.8 52.4 0.5 C14 A:21G602 4.8 70.0 0.5 CG A:HIS285 4.8 61.8 0.5 C I:GLU282 4.8 54.3 1.0 C27 A:21G602 4.8 81.7 0.5 N12 A:21G602 4.9 68.1 0.5 O I:GLU282 5.0 58.0 1.0 C7 A:21G602 5.0 66.5 0.5

Fluorine binding site 7 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:33.6 occ:1.00 F31 C:21G601 0.0 33.6 1.0 C14 C:21G601 1.3 31.6 1.0 C13 C:21G601 2.3 32.5 1.0 C15 C:21G601 2.4 32.0 1.0 N17 C:21G601 2.8 30.7 1.0 CB C:ASN510 3.3 35.0 1.0 O C:VAL511 3.4 35.5 1.0 CD2 C:LEU512 3.4 36.3 1.0 CG C:PHE323 3.4 35.1 1.0 CB C:PHE323 3.5 36.4 1.0 CD2 C:PHE323 3.5 34.7 1.0 N12 C:21G601 3.5 34.6 1.0 N16 C:21G601 3.6 32.7 1.0 C C:VAL511 3.7 36.6 1.0 CA C:LEU512 3.9 35.8 1.0 C C:ASN510 4.0 35.6 1.0 N C:LEU512 4.0 37.5 1.0 C11 C:21G601 4.0 32.2 1.0 O C:ASN510 4.1 33.9 1.0 CD1 C:PHE323 4.1 35.1 1.0 C18 C:21G601 4.2 31.8 1.0 CG C:LEU512 4.3 37.0 1.0 CE2 C:PHE323 4.3 33.5 1.0 N C:VAL511 4.3 36.6 1.0 CA C:ASN510 4.3 34.6 1.0 CG C:ASN510 4.4 34.0 1.0 CB C:LEU512 4.6 37.0 1.0 CA C:VAL511 4.7 34.5 1.0 OD2 C:ASP506 4.7 43.8 1.0 ND2 C:ASN510 4.7 35.4 1.0 CE1 C:PHE323 4.8 34.8 1.0 CZ C:PHE323 4.8 33.9 1.0 CA C:PHE323 4.9 36.8 1.0 C20 C:21G601 5.0 32.1 1.0 C25 C:21G601 5.0 31.9 1.0

Fluorine binding site 8 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:31.0 occ:1.00 F32 C:21G601 0.0 31.0 1.0 C2 C:21G601 1.3 30.1 1.0 C1 C:21G601 2.3 29.7 1.0 C3 C:21G601 2.4 32.4 1.0 NE2 C:GLN406 3.1 32.5 1.0 CE C:MET431 3.4 37.6 1.0 CD C:GLN406 3.5 32.7 1.0 C6 C:21G601 3.6 30.8 1.0 O C:PHE404 3.6 37.3 1.0 N4 C:21G601 3.6 32.1 1.0 CG C:GLN406 3.9 32.6 1.0 C26 C:21G601 4.0 30.8 1.0 CD1 C:PHE404 4.1 33.4 1.0 C5 C:21G601 4.1 30.9 1.0 SD C:MET431 4.1 37.3 1.0 OE1 C:GLN406 4.1 32.0 1.0 CE1 C:PHE404 4.2 34.1 1.0 CD2 C:HIS357 4.4 29.1 1.0 C C:PHE404 4.5 35.8 1.0 CA C:PHE404 4.5 35.2 1.0 C27 C:21G601 4.5 31.5 1.0 CG C:MET431 4.5 36.5 1.0 CG C:PHE404 4.6 34.0 1.0 CZ C:PHE404 4.9 33.9 1.0 O C:ARG355 4.9 33.2 1.0 C7 C:21G601 4.9 29.4 1.0 NE2 C:HIS357 5.0 29.8 1.0 C25 C:21G601 5.0 31.9 1.0

Fluorine binding site 9 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:51.6 occ:0.50 F31 C:21G602 0.0 51.6 0.5 C14 C:21G602 1.3 53.0 0.5 C15 C:21G602 2.3 53.8 0.5 C13 C:21G602 2.4 54.2 0.5 N17 C:21G602 2.6 55.2 0.5 CG F:GLU282 2.9 63.7 1.0 N4 C:21G602 3.3 53.3 0.5 CD F:GLU282 3.4 74.1 1.0 OE2 F:GLU282 3.5 79.9 1.0 N16 C:21G602 3.6 54.2 0.5 N12 C:21G602 3.6 54.8 0.5 CB F:GLU282 3.8 57.7 1.0 C3 C:21G602 3.9 52.9 0.5 C18 C:21G602 4.0 56.9 0.5 C11 C:21G602 4.0 52.2 0.5 C5 C:21G602 4.1 54.0 0.5 OE1 F:GLU282 4.2 86.4 1.0 CA F:GLU282 4.2 51.6 1.0 C24 C:21G602 4.4 55.9 0.5 N9 C:21G602 4.5 52.3 0.5 C20 C:21G602 4.5 56.6 0.5 C25 C:21G602 4.7 56.8 0.5 NE2 C:HIS285 4.8 60.4 0.5 C23 C:21G602 4.8 55.5 0.5 CD2 F:HIS285 4.9 53.0 0.5 O F:GLU282 4.9 46.3 1.0

Fluorine binding site 10 out of 16 in the Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of the Midlink and Cap-Binding Domains of Influenza A Polymerase PB2 Subunit with A Bound Azaindole Cap-Binding Inhibitor (Vx-787) within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:53.9 occ:0.50 F31 C:21G602 0.0 53.9 0.5 C14 C:21G602 1.3 56.5 0.5 C13 C:21G602 2.3 58.2 0.5 C15 C:21G602 2.4 57.5 0.5 N4 C:21G602 2.7 50.5 0.5 N17 C:21G602 2.8 58.9 0.5 C3 C:21G602 2.9 48.7 0.5 OE2 C:GLU282 3.2 74.2 1.0 N12 C:21G602 3.5 58.4 0.5 CD C:GLU282 3.6 69.8 1.0 N16 C:21G602 3.6 57.7 0.5 O C:HOH704 3.6 32.6 1.0 CG C:GLU282 3.6 64.4 1.0 C5 C:21G602 3.8 50.5 0.5 C11 C:21G602 4.0 56.2 0.5 C2 C:21G602 4.2 47.4 0.5 C18 C:21G602 4.3 57.3 0.5 OE1 C:GLU282 4.4 65.6 1.0 N9 C:21G602 4.5 50.4 0.5 CB C:GLU282 4.7 60.3 1.0 O30 C:21G602 4.8 53.5 0.5 C20 C:21G602 4.9 57.8 0.5 C6 C:21G602 4.9 50.5 0.5 F32 C:21G602 5.0 46.0 0.5

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