Manganese in PDB 5wf3: Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023), PDB code: 5wf3 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)	32.06 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.679, 90.679, 133.752, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.7

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023) (pdb code 5wf3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023), PDB code: 5wf3:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:63.5 occ:1.00 NE2 A:HIS41 2.1 57.5 1.0 OD1 A:ASP108 2.1 52.9 1.0 O2 A:KU2205 2.1 60.4 1.0 O A:ILE120 2.2 61.4 1.0 OD1 A:ASP119 2.3 72.8 1.0 O1 A:KU2205 2.3 70.1 1.0 C4 A:KU2205 2.9 71.0 1.0 CE1 A:HIS41 2.9 56.9 1.0 C3 A:KU2205 3.0 75.2 1.0 CG A:ASP108 3.0 58.8 1.0 OD2 A:ASP108 3.2 58.5 1.0 CD2 A:HIS41 3.2 54.9 1.0 C A:ILE120 3.3 58.5 1.0 CG A:ASP119 3.4 71.9 1.0 N A:ILE120 3.6 50.5 1.0 MN A:MN202 3.9 81.9 1.0 O A:HOH301 3.9 58.1 1.0 OD2 A:ASP119 3.9 78.4 1.0 CA A:ILE120 4.0 49.6 1.0 ND1 A:HIS41 4.1 53.2 1.0 N2 A:KU2205 4.2 80.3 1.0 C A:ASP119 4.2 60.4 1.0 CG A:HIS41 4.3 58.5 1.0 C2 A:KU2205 4.3 80.2 1.0 N A:GLY121 4.4 60.8 1.0 CB A:ASP108 4.4 51.4 1.0 CB A:ILE120 4.5 55.9 1.0 CA A:ASP119 4.5 60.0 1.0 CB A:ASP119 4.6 67.3 1.0 O A:HOH308 4.7 67.9 1.0 CA A:GLY121 4.7 55.9 1.0 O3 A:KU2205 4.9 85.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9K (Sri-30023) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:81.9 occ:1.00 O3 A:KU2205 2.0 85.2 1.0 OD2 A:ASP108 2.2 58.5 1.0 O1 A:KU2205 2.2 70.1 1.0 OE1 A:GLU80 2.3 70.3 1.0 O A:HOH301 2.4 58.1 1.0 O A:HOH302 2.6 76.9 1.0 C5 A:KU2205 3.1 84.9 1.0 C3 A:KU2205 3.3 75.2 1.0 CG A:ASP108 3.4 58.8 1.0 CD A:GLU80 3.5 68.7 1.0 C2 A:KU2205 3.7 80.2 1.0 MN A:MN201 3.9 63.5 1.0 OD1 A:ASP108 3.9 52.9 1.0 CE1 A:HIS41 3.9 56.9 1.0 O A:PRO107 4.1 64.7 1.0 O A:LEU106 4.2 66.1 1.0 N3 A:KU2205 4.3 89.2 1.0 CG A:GLU80 4.3 56.9 1.0 C A:PRO107 4.4 63.2 1.0 OE2 A:GLU80 4.4 75.7 1.0 CB A:GLU80 4.4 53.5 1.0 CB A:ASP108 4.5 51.4 1.0 CA A:ASP108 4.5 52.5 1.0 NE2 A:HIS41 4.5 57.5 1.0 C4 A:KU2205 4.6 71.0 1.0 N A:ASP108 4.6 58.2 1.0 C14 A:KU2205 4.7 0.6 1.0 C12 A:KU2205 4.7 94.6 1.0 ND1 A:HIS41 4.9 53.2 1.0 OD1 A:ASP119 4.9 72.8 1.0 OD2 A:ASP119 4.9 78.4 1.0 C A:LEU106 5.0 68.0 1.0 O2 A:KU2205 5.0 60.4 1.0 N1 A:KU2205 5.0 83.5 1.0

D.Beylkin, G.Kumar, W.Zhou, J.Park, T.Jeevan, C.Lagisetti, R.Harfoot, R.J.Webby, S.W.White, T.R.Webb. Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Sci Rep V. 7 17139 2017.
ISSN: ESSN 2045-2322
PubMed: 29215062
DOI: 10.1038/S41598-017-17419-6