Magnesium in PDB 6ya5: 2009 H1N1 Pa Endonuclease in Complex with LU2

The structure of 2009 H1N1 Pa Endonuclease in Complex with LU2, PDB code: 6ya5 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)	42.57 / 2.00
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.069, 74.069, 127.715, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 26.4

The structure of 2009 H1N1 Pa Endonuclease in Complex with LU2 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the 2009 H1N1 Pa Endonuclease in Complex with LU2 (pdb code 6ya5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 2009 H1N1 Pa Endonuclease in Complex with LU2, PDB code: 6ya5:

Magnesium binding site 1 out of 1 in the 2009 H1N1 Pa Endonuclease in Complex with LU2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2009 H1N1 Pa Endonuclease in Complex with LU2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.9 occ:1.00 O A:HOH315 2.0 27.5 1.0 OD1 A:ASP108 2.0 27.9 1.0 OE2 A:GLU80 2.0 26.6 1.0 O5 A:LU2203 2.1 30.8 1.0 O A:HOH328 2.1 27.8 1.0 O A:HOH325 2.2 26.1 1.0 CG A:ASP108 3.1 29.7 1.0 CD A:GLU80 3.2 31.4 1.0 C12 A:LU2203 3.2 32.7 1.0 C11 A:LU2203 3.6 33.3 1.0 MN A:MN201 3.7 34.7 1.0 OD2 A:ASP108 3.7 27.2 1.0 CE1 A:HIS41 3.9 24.8 1.0 O A:HOH321 4.1 31.9 1.0 CG A:GLU80 4.1 31.7 1.0 OE1 A:GLU80 4.1 30.8 1.0 O A:HOH333 4.1 33.2 1.0 O A:LEU106 4.2 30.5 1.0 O A:PRO107 4.2 29.2 1.0 OE1 A:GLU119 4.2 31.6 1.0 O A:HOH373 4.3 35.6 1.0 CB A:GLU80 4.3 31.5 1.0 O A:DMS206 4.3 62.3 1.0 CB A:ASP108 4.3 31.7 1.0 OE2 A:GLU119 4.4 31.1 1.0 CA A:ASP108 4.4 28.6 1.0 NE2 A:HIS41 4.4 28.3 1.0 C A:PRO107 4.4 28.3 1.0 C13 A:LU2203 4.4 32.8 1.0 N A:ASP108 4.5 29.8 1.0 CD A:GLU119 4.8 33.8 1.0 O6 A:LU2203 4.8 28.7 1.0 CA A:GLU80 4.8 30.5 1.0 S A:DMS206 4.8 74.3 0.9 C10 A:LU2203 4.9 35.4 1.0

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