Manganese in PDB 5wfw: Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10J (Sri-30026)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10J (Sri-30026), PDB code: 5wfw 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)	31.97 / 2.29
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.425, 90.425, 133.813, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 22.4

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10J (Sri-30026) 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 10J (Sri-30026) (pdb code 5wfw). 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 10J (Sri-30026), PDB code: 5wfw:
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 10J (Sri-30026)


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 10J (Sri-30026) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:68.2 occ:1.00 O2 A:GYA205 1.9 78.0 1.0 OD2 A:ASP108 2.2 65.3 1.0 NE2 A:HIS41 2.2 60.9 1.0 O A:ILE120 2.2 61.9 1.0 O1 A:GYA205 2.4 87.2 1.0 OD1 A:ASP119 2.4 84.4 1.0 C2 A:GYA205 2.8 85.5 1.0 CE1 A:HIS41 2.9 61.6 1.0 C1 A:GYA205 2.9 87.8 1.0 CG A:ASP108 3.1 70.2 1.0 OD1 A:ASP108 3.3 70.1 1.0 C A:ILE120 3.4 58.5 1.0 CD2 A:HIS41 3.4 61.6 1.0 N A:ILE120 3.5 55.4 1.0 CG A:ASP119 3.6 88.0 1.0 MN A:MN202 3.8 81.9 1.0 O A:HOH302 3.9 54.0 1.0 CA A:ILE120 4.0 58.2 1.0 ND1 A:HIS41 4.1 57.5 1.0 C3 A:GYA205 4.1 88.8 1.0 OD2 A:ASP119 4.2 91.8 1.0 C A:ASP119 4.2 62.8 1.0 NZ A:LYS134 4.3 79.7 1.0 N4 A:GYA205 4.3 90.7 1.0 CG A:HIS41 4.4 62.0 1.0 O5 A:GYA205 4.4 90.6 1.0 N A:GLY121 4.4 66.6 1.0 CB A:ASP108 4.5 62.6 1.0 CB A:ILE120 4.5 59.3 1.0 CA A:ASP119 4.5 68.8 1.0 O A:HOH305 4.6 67.8 1.0 CB A:ASP119 4.6 80.6 1.0 C4 A:GYA205 4.8 91.3 1.0 CA A:GLY121 4.8 61.1 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 10J (Sri-30026)


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 10J (Sri-30026) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:81.9 occ:1.00 O5 A:GYA205 1.8 90.6 1.0 OD1 A:ASP108 2.0 70.1 1.0 O A:HOH302 2.3 54.0 1.0 OE1 A:GLU80 2.4 59.7 1.0 O A:HOH301 2.5 66.7 1.0 O2 A:GYA205 2.6 78.0 1.0 C4 A:GYA205 3.0 91.3 1.0 CG A:ASP108 3.2 70.2 1.0 CD A:GLU80 3.5 65.3 1.0 C2 A:GYA205 3.5 85.5 1.0 C3 A:GYA205 3.7 88.8 1.0 OD2 A:ASP108 3.8 65.3 1.0 MN A:MN201 3.8 68.2 1.0 CE1 A:HIS41 3.9 61.6 1.0 N1 A:GYA205 4.0 92.9 1.0 O A:PRO107 4.2 60.3 1.0 CG A:GLU80 4.2 61.0 1.0 C5 A:GYA205 4.3 95.5 1.0 O A:LEU106 4.3 73.7 1.0 CB A:GLU80 4.3 59.8 1.0 CB A:ASP108 4.4 62.6 1.0 OE2 A:GLU80 4.4 72.0 1.0 C A:PRO107 4.4 63.7 1.0 CA A:ASP108 4.4 60.1 1.0 N A:ASP108 4.5 59.0 1.0 NE2 A:HIS41 4.6 60.9 1.0 ND1 A:HIS41 4.7 57.5 1.0 C1 A:GYA205 4.8 87.8 1.0 OD1 A:ASP119 4.8 84.4 1.0 CA A:GLU80 5.0 57.8 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