Manganese in PDB 5ega: 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor

The structure of 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor, PDB code: 5ega 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)	50.00 / 2.15
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.989, 73.989, 128.546, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 23.4

The binding sites of Manganese atom in the 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor (pdb code 5ega). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor, PDB code: 5ega:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:47.4 occ:1.00 O10 A:GK0303 1.9 53.7 1.0 O A:ILE120 2.2 45.6 1.0 OD2 A:ASP108 2.2 41.1 1.0 O13 A:GK0303 2.2 46.0 1.0 OE1 A:GLU119 2.3 50.2 1.0 NE2 A:HIS41 2.4 45.4 1.0 C09 A:GK0303 2.9 52.5 1.0 C12 A:GK0303 3.1 57.0 1.0 CG A:ASP108 3.1 44.8 1.0 CE1 A:HIS41 3.2 46.2 1.0 CD A:GLU119 3.3 48.8 1.0 OD1 A:ASP108 3.3 43.7 1.0 C A:ILE120 3.3 49.1 1.0 CD2 A:HIS41 3.4 47.5 1.0 MN A:MN302 3.6 66.8 1.0 OE2 A:GLU119 3.7 50.9 1.0 N A:ILE120 3.7 49.5 1.0 CA A:ILE120 4.0 50.2 1.0 O A:HOH401 4.0 41.7 1.0 NZ A:LYS134 4.2 68.5 1.0 C06 A:GK0303 4.2 58.3 1.0 CB A:ILE120 4.3 52.5 1.0 ND1 A:HIS41 4.3 44.0 1.0 N A:GLY121 4.4 49.3 1.0 O A:HOH407 4.4 48.2 1.0 C01 A:GK0303 4.4 61.7 1.0 CG A:HIS41 4.4 45.2 1.0 CG A:GLU119 4.4 47.1 1.0 CB A:ASP108 4.5 44.2 1.0 CE A:LYS134 4.5 69.8 1.0 C A:GLU119 4.7 50.6 1.0 CA A:GLY121 4.7 48.1 1.0 OE1 A:GLU80 4.7 41.7 1.0 O07 A:GK0303 4.8 54.3 1.0 SG A:CYS45 4.9 46.2 1.0 CG2 A:ILE120 4.9 52.4 1.0

Manganese binding site 2 out of 2 in the 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2009 H1N1 Pa Endonuclease Domain in Complex with An N-Acylhydrazone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:66.8 occ:1.00 OD1 A:ASP108 2.1 43.7 1.0 O10 A:GK0303 2.2 53.7 1.0 O A:HOH401 2.2 41.7 1.0 O07 A:GK0303 2.2 54.3 1.0 OE1 A:GLU80 2.2 41.7 1.0 O A:HOH417 2.3 43.9 1.0 C09 A:GK0303 2.9 52.5 1.0 C06 A:GK0303 3.0 58.3 1.0 CG A:ASP108 3.2 44.8 1.0 CD A:GLU80 3.3 48.0 1.0 MN A:MN301 3.6 47.4 1.0 OD2 A:ASP108 3.7 41.1 1.0 CE1 A:HIS41 3.9 46.2 1.0 CG A:GLU80 4.1 46.5 1.0 OE2 A:GLU119 4.2 50.9 1.0 OE2 A:GLU80 4.2 49.4 1.0 O A:HOH429 4.2 53.3 1.0 C12 A:GK0303 4.2 57.0 1.0 O A:PRO107 4.3 41.5 1.0 CB A:GLU80 4.3 46.0 1.0 C04 A:GK0303 4.3 63.1 1.0 NE2 A:HIS41 4.4 45.4 1.0 O A:LEU106 4.4 45.9 1.0 CB A:ASP108 4.4 44.2 1.0 C A:PRO107 4.4 46.0 1.0 CA A:ASP108 4.4 41.7 1.0 OE1 A:GLU119 4.5 50.2 1.0 N A:ASP108 4.5 41.7 1.0 O13 A:GK0303 4.7 46.0 1.0 CD A:GLU119 4.8 48.8 1.0 CA A:GLU80 4.9 43.2 1.0

M.Carcelli, D.Rogolino, A.Gatti, L.De Luca, M.Sechi, G.Kumar, S.W.White, A.Stevaert, L.Naesens. N-Acylhydrazone Inhibitors of Influenza Virus Pa Endonuclease with Versatile Metal Binding Modes. Sci Rep V. 6 31500 2016.
ISSN: ESSN 2045-2322
PubMed: 27510745
DOI: 10.1038/SREP31500