Manganese in PDB 5w73: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9F (Sri-29835)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9F (Sri-29835), PDB code: 5w73 was solved by G.Kumar, S.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.24 / 2.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.843, 89.843, 135.002, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.8

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9F (Sri-29835) 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 in Complex with Inhibitor 9F (Sri-29835) (pdb code 5w73). 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 in Complex with Inhibitor 9F (Sri-29835), PDB code: 5w73:
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 in Complex with Inhibitor 9F (Sri-29835)


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 in Complex with Inhibitor 9F (Sri-29835) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:68.2 occ:1.00 O2 A:GY9205 2.0 72.8 1.0 OE2 A:GLU119 2.1 76.7 1.0 OD2 A:ASP108 2.2 66.5 1.0 O A:ILE120 2.2 73.8 1.0 O1 A:GY9205 2.3 85.2 1.0 NE2 A:HIS41 2.3 70.7 1.0 C4 A:GY9205 2.7 82.9 1.0 C3 A:GY9205 2.9 86.4 1.0 CG A:ASP108 3.0 65.8 1.0 CD A:GLU119 3.1 81.8 1.0 OD1 A:ASP108 3.1 66.6 1.0 CD2 A:HIS41 3.2 58.4 1.0 CE1 A:HIS41 3.3 68.2 1.0 OE1 A:GLU119 3.3 71.4 1.0 C A:ILE120 3.4 72.5 1.0 N A:ILE120 3.7 64.3 1.0 MN A:MN202 3.7 82.1 1.0 O A:HOH302 3.9 54.0 1.0 CA A:ILE120 4.0 63.5 1.0 N2 A:GY9205 4.0 88.1 1.0 O A:HOH303 4.3 63.4 1.0 C2 A:GY9205 4.3 91.0 1.0 CG A:HIS41 4.4 70.0 1.0 ND1 A:HIS41 4.4 71.7 1.0 CB A:ASP108 4.4 58.9 1.0 N A:GLY121 4.4 78.0 1.0 CG A:GLU119 4.5 70.8 1.0 CB A:ILE120 4.5 78.0 1.0 C A:GLU119 4.6 76.1 1.0 CA A:GLY121 4.7 67.2 1.0 CE A:LYS134 4.9 0.1 1.0 O3 A:GY9205 4.9 87.1 1.0 CA A:GLU119 5.0 72.0 1.0 OE1 A:GLU80 5.0 72.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9F (Sri-29835)


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 in Complex with Inhibitor 9F (Sri-29835) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:82.1 occ:1.00 O A:HOH305 1.8 59.1 1.0 O1 A:GY9205 2.0 85.2 1.0 OD1 A:ASP108 2.1 66.6 1.0 O3 A:GY9205 2.1 87.1 1.0 O A:HOH302 2.2 54.0 1.0 OE1 A:GLU80 2.3 72.1 1.0 C3 A:GY9205 3.1 86.4 1.0 C5 A:GY9205 3.1 90.0 1.0 CG A:ASP108 3.2 65.8 1.0 CD A:GLU80 3.5 72.5 1.0 C2 A:GY9205 3.6 91.0 1.0 CE1 A:HIS41 3.7 68.2 1.0 MN A:MN201 3.7 68.2 1.0 OD2 A:ASP108 3.8 66.5 1.0 NE2 A:HIS41 4.1 70.7 1.0 CG A:GLU80 4.2 62.8 1.0 O A:PRO107 4.3 69.5 1.0 OE1 A:GLU119 4.3 71.4 1.0 CB A:GLU80 4.3 63.4 1.0 O A:LEU106 4.3 67.9 1.0 C4 A:GY9205 4.3 82.9 1.0 N3 A:GY9205 4.4 90.8 1.0 CB A:ASP108 4.4 58.9 1.0 OE2 A:GLU80 4.4 77.3 1.0 C A:PRO107 4.5 73.5 1.0 CA A:ASP108 4.5 61.3 1.0 N A:ASP108 4.6 61.8 1.0 O2 A:GY9205 4.7 72.8 1.0 ND1 A:HIS41 4.8 71.7 1.0 C12 A:GY9205 4.9 94.9 1.0 N1 A:GY9205 4.9 98.5 1.0 OE2 A:GLU119 5.0 76.7 1.0 CA A:GLU80 5.0 65.1 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