Nickel 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:

Fluorine

(F)

16 atoms

The binding sites of Nickel 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 Nickel atom.
In total 4 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 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 Nickel with other atoms in the Ni 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:Ni603 b:64.4 occ:1.00 ND1 A:HIS432 2.1 37.3 1.0 O A:HOH711 2.6 20.9 1.0 O A:HOH718 2.6 34.6 1.0 O A:HOH710 2.7 24.7 1.0 CE1 A:HIS432 3.0 36.8 1.0 CG A:HIS432 3.1 35.5 1.0 CB A:HIS432 3.5 34.7 1.0 CB A:ASN429 3.9 48.1 1.0 N A:HIS432 4.0 32.6 1.0 O A:ASN429 4.1 39.0 1.0 NE2 A:HIS432 4.1 34.0 1.0 CD2 A:HIS432 4.2 35.1 1.0 CA A:HIS432 4.3 34.2 1.0 N A:ASN429 4.5 44.8 1.0 CA A:ASN429 4.5 45.6 1.0 C23 A:21G601 4.5 36.0 1.0 C A:ASN429 4.5 42.4 1.0 C22 A:21G601 4.6 34.7 1.0 ND2 A:ASN429 4.9 57.7 1.0 CG A:ASN429 5.0 54.4 1.0

Nickel binding site 2 out of 4 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 Nickel with other atoms in the Ni 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 C:Ni603 b:68.9 occ:1.00 ND1 C:HIS432 2.0 40.2 1.0 O C:HOH716 2.3 14.9 1.0 O C:HOH725 2.7 24.1 1.0 O C:HOH723 2.8 29.2 1.0 CG C:HIS432 3.0 39.3 1.0 CE1 C:HIS432 3.1 42.8 1.0 CB C:HIS432 3.2 38.8 1.0 N C:HIS432 3.7 37.5 1.0 O C:ASN429 3.8 42.8 1.0 CB C:ASN429 3.9 54.7 1.0 CA C:HIS432 4.1 38.9 1.0 CD2 C:HIS432 4.1 42.4 1.0 NE2 C:HIS432 4.2 44.1 1.0 C C:ASN429 4.3 48.4 1.0 N C:ASN429 4.3 51.4 1.0 CA C:ASN429 4.3 51.0 1.0 C C:MET431 4.8 37.6 1.0 C22 C:21G601 4.8 31.7 1.0 C23 C:21G601 4.9 31.6 1.0 N C:MET431 4.9 41.4 1.0 CB C:MET431 5.0 36.4 1.0

Nickel binding site 3 out of 4 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 Nickel with other atoms in the Ni 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 F:Ni602 b:84.8 occ:1.00 ND1 F:HIS432 2.1 42.1 1.0 O F:HOH722 2.5 33.8 1.0 O F:HOH725 2.8 44.8 1.0 CE1 F:HIS432 3.0 42.8 1.0 CG F:HIS432 3.1 41.4 1.0 CB F:HIS432 3.4 40.0 1.0 CB F:ASN429 3.8 40.7 1.0 N F:HIS432 4.0 34.5 1.0 O F:ASN429 4.0 38.6 1.0 NE2 F:HIS432 4.1 41.9 1.0 CD2 F:HIS432 4.2 40.6 1.0 CA F:HIS432 4.3 37.5 1.0 N F:ASN429 4.4 42.4 1.0 CA F:ASN429 4.4 40.5 1.0 C F:ASN429 4.5 38.5 1.0 C22 F:21G601 4.7 32.9 1.0 ND2 F:ASN429 4.7 43.4 1.0 C23 F:21G601 4.8 35.8 1.0 CG F:ASN429 4.8 41.8 1.0

Nickel binding site 4 out of 4 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 Nickel with other atoms in the Ni 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 I:Ni602 b:77.6 occ:1.00 ND1 I:HIS432 2.0 44.1 1.0 O I:HOH715 2.1 30.3 1.0 O I:HOH711 2.4 34.4 1.0 O I:HOH725 2.6 23.8 1.0 CE1 I:HIS432 3.0 48.3 1.0 CG I:HIS432 3.0 41.5 1.0 CB I:HIS432 3.4 39.2 1.0 CB I:ASN429 4.0 48.1 1.0 NE2 I:HIS432 4.1 48.8 1.0 CD2 I:HIS432 4.1 43.4 1.0 O I:ASN429 4.2 46.2 1.0 N I:ASN429 4.3 45.6 1.0 N I:HIS432 4.3 38.2 1.0 CA I:HIS432 4.4 38.8 1.0 CA I:ASN429 4.5 45.3 1.0 C I:ASN429 4.6 46.0 1.0 C23 I:21G601 4.9 33.2 1.0 ND2 I:ASN429 4.9 47.2 1.0 CG I:ASN429 5.0 49.4 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