Manganese in PDB 6yem: H1N1 2009 Pa Endonuclease in Complex with Quambalarine B

The structure of H1N1 2009 Pa Endonuclease in Complex with Quambalarine B, PDB code: 6yem was solved by K.Radilova, J.Brynda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.21 / 2.50
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.340, 73.340, 128.750, 90.00, 90.00, 120.00
R / Rfree (%)	26.1 / 31.8

The structure of H1N1 2009 Pa Endonuclease in Complex with Quambalarine B also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Manganese atom in the H1N1 2009 Pa Endonuclease in Complex with Quambalarine B (pdb code 6yem). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the H1N1 2009 Pa Endonuclease in Complex with Quambalarine B, PDB code: 6yem:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the H1N1 2009 Pa Endonuclease in Complex with Quambalarine B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of H1N1 2009 Pa Endonuclease in Complex with Quambalarine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:0.2 occ:0.74 O6 A:OOH205 1.9 75.9 0.8 OD2 A:ASP108 2.0 55.6 0.8 O A:OOH205 2.0 67.5 0.8 O A:ILE120 2.1 62.5 1.0 NE2 A:HIS41 2.5 56.4 1.0 C A:OOH205 2.5 75.3 0.8 C5 A:OOH205 2.6 70.6 0.8 CG A:ASP108 3.0 60.3 1.0 OE2 A:GLU119 3.2 80.8 1.0 C A:ILE120 3.2 57.5 1.0 CE1 A:HIS41 3.4 58.9 1.0 OD1 A:ASP108 3.4 63.0 1.0 OE1 A:GLU119 3.4 83.3 1.0 CD2 A:HIS41 3.5 57.0 1.0 N A:ILE120 3.5 58.8 1.0 CD A:GLU119 3.6 77.3 1.0 MN A:MN202 3.8 0.4 0.5 CA A:ILE120 3.9 59.7 1.0 C1 A:OOH205 3.9 74.5 0.8 C4 A:OOH205 3.9 67.8 0.8 NZ A:LYS134 4.1 83.8 0.7 O A:HOH301 4.2 51.3 1.0 CB A:ILE120 4.3 58.4 1.0 N A:GLY121 4.3 59.2 1.0 CB A:ASP108 4.3 58.1 1.0 ND1 A:HIS41 4.4 61.6 1.0 O1 A:OOH205 4.5 58.5 0.8 C A:GLU119 4.5 63.3 1.0 CG A:HIS41 4.5 56.8 1.0 CA A:GLY121 4.6 56.3 1.0 OE2 A:GLU80 4.6 51.9 1.0 C6 A:OOH205 4.7 67.6 0.8 CA A:GLU119 4.8 64.3 1.0 CG A:GLU119 4.9 74.0 1.0 C2 A:OOH205 4.9 73.4 0.8 C3 A:OOH205 4.9 72.4 0.8 CG2 A:ILE120 5.0 55.1 1.0

Manganese binding site 2 out of 2 in the H1N1 2009 Pa Endonuclease in Complex with Quambalarine B


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of H1N1 2009 Pa Endonuclease in Complex with Quambalarine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:0.4 occ:0.52 OE2 A:GLU80 1.7 51.9 1.0 OD1 A:ASP108 2.0 63.0 1.0 O1 A:OOH205 2.0 58.5 0.8 O A:HOH301 2.1 51.3 1.0 O A:HOH302 2.3 55.9 1.0 O A:OOH205 2.3 67.5 0.8 CD A:GLU80 2.9 54.7 1.0 CG A:ASP108 3.1 60.3 1.0 C6 A:OOH205 3.1 67.6 0.8 C5 A:OOH205 3.4 70.6 0.8 OD2 A:ASP108 3.5 55.6 0.8 CE1 A:HIS41 3.7 58.9 1.0 OE1 A:GLU80 3.7 56.2 1.0 C4 A:OOH205 3.7 67.8 0.8 MN A:MN201 3.8 0.2 0.7 CG A:GLU80 3.8 50.0 1.0 OE1 A:GLU119 3.9 83.3 1.0 CB A:GLU80 4.1 53.2 1.0 O A:PRO107 4.2 58.1 1.0 NE2 A:HIS41 4.2 56.4 1.0 CB A:ASP108 4.3 58.1 1.0 C7 A:OOH205 4.4 71.3 0.8 CA A:ASP108 4.5 54.4 1.0 C A:PRO107 4.5 54.0 1.0 O4 A:OOH205 4.6 71.2 0.8 C A:OOH205 4.6 75.3 0.8 N A:ASP108 4.7 58.7 1.0 O A:LEU106 4.7 54.3 1.0 ND1 A:HIS41 4.7 61.6 1.0 CA A:GLU80 4.7 53.4 1.0 CD A:GLU119 4.9 77.3 1.0 O A:HOH310 5.0 61.6 1.0 O6 A:OOH205 5.0 75.9 0.8

V.Zima, K.Radilova, M.Kozisek, C.B.Albinana, E.Karlukova, J.Brynda, J.Fanfrlik, M.Flieger, J.Hodek, J.Weber, P.Majer, J.Konvalinka, A.Machara. Unraveling the Anti-Influenza Effect of Flavonoids: Experimental Validation of Luteolin and Its Congeners As Potent Influenza Endonuclease Inhibitors. Eur.J.Med.Chem. V. 208 12754 2020.
ISSN: ISSN 0223-5234
PubMed: 32883638
DOI: 10.1016/J.EJMECH.2020.112754