Manganese in PDB 5wfz: Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 8E (Sri-30049)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 8E (Sri-30049), PDB code: 5wfz 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)	31.93 / 2.35
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.300, 90.300, 133.353, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 22.7

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 8E (Sri-30049) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 8E (Sri-30049) (pdb code 5wfz). 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 8E (Sri-30049), PDB code: 5wfz:
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 8E (Sri-30049)


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 8E (Sri-30049) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:50.1 occ:1.00 OD2 A:ASP108 2.2 51.8 1.0 O A:ILE120 2.2 53.9 1.0 O6 A:KU0205 2.2 66.9 1.0 NE2 A:HIS41 2.2 47.8 1.0 O5 A:KU0205 2.2 68.0 1.0 OD1 A:ASP119 2.5 55.8 1.0 CE1 A:HIS41 2.8 46.4 1.0 C17 A:KU0205 2.9 75.2 1.0 C16 A:KU0205 3.0 73.6 1.0 CG A:ASP108 3.0 54.9 1.0 OD1 A:ASP108 3.2 58.6 1.0 C A:ILE120 3.3 50.5 1.0 CD2 A:HIS41 3.3 47.1 1.0 N A:ILE120 3.6 44.9 1.0 MN A:MN202 3.7 63.4 1.0 CG A:ASP119 3.7 57.4 1.0 O A:HOH307 3.8 43.0 1.0 CA A:ILE120 4.0 46.7 1.0 ND1 A:HIS41 4.0 46.3 1.0 N4 A:KU0205 4.2 84.0 1.0 C A:ASP119 4.3 48.2 1.0 CG A:HIS41 4.3 47.6 1.0 C6 A:KU0205 4.3 79.3 1.0 NZ A:LYS134 4.3 72.4 1.0 N A:GLY121 4.4 51.7 1.0 OD2 A:ASP119 4.4 60.0 1.0 CB A:ASP108 4.4 53.4 1.0 CB A:ILE120 4.5 45.2 1.0 CA A:ASP119 4.6 50.6 1.0 CA A:GLY121 4.7 49.9 1.0 CB A:ASP119 4.7 55.2 1.0 O A:HOH322 4.8 62.5 1.0 O2 A:KU0205 4.8 73.3 1.0 CE A:LYS134 4.8 73.2 1.0 OE1 A:GLU80 5.0 54.6 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 8E (Sri-30049)


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 8E (Sri-30049) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:63.4 occ:1.00 O2 A:KU0205 1.9 73.3 1.0 OD1 A:ASP108 2.1 58.6 1.0 O5 A:KU0205 2.2 68.0 1.0 O A:HOH302 2.2 64.6 1.0 OE1 A:GLU80 2.3 54.6 1.0 O A:HOH307 2.4 43.0 1.0 C7 A:KU0205 2.9 79.9 1.0 C16 A:KU0205 3.1 73.6 1.0 CG A:ASP108 3.2 54.9 1.0 CD A:GLU80 3.4 53.7 1.0 C6 A:KU0205 3.5 79.3 1.0 MN A:MN201 3.7 50.1 1.0 OD2 A:ASP108 3.8 51.8 1.0 CE1 A:HIS41 3.9 46.4 1.0 O A:PRO107 4.1 54.3 1.0 N3 A:KU0205 4.1 87.3 1.0 CG A:GLU80 4.2 48.6 1.0 OE2 A:GLU80 4.3 56.9 1.0 O A:LEU106 4.3 59.6 1.0 CB A:ASP108 4.3 53.4 1.0 CB A:GLU80 4.3 46.5 1.0 C A:PRO107 4.3 55.0 1.0 C17 A:KU0205 4.4 75.2 1.0 CA A:ASP108 4.4 53.1 1.0 N A:ASP108 4.5 55.0 1.0 OD1 A:ASP119 4.6 55.8 1.0 NE2 A:HIS41 4.6 47.8 1.0 C8 A:KU0205 4.6 96.6 1.0 C11 A:KU0205 4.7 0.1 1.0 C9 A:KU0205 4.7 0.0 1.0 O6 A:KU0205 4.8 66.9 1.0 N2 A:KU0205 4.8 85.2 1.0 ND1 A:HIS41 4.8 46.3 1.0 C12 A:KU0205 5.0 0.7 1.0 CA A:GLU80 5.0 49.2 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