Manganese in PDB 7nug: Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin

The structure of Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin, PDB code: 7nug 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)	42.15 / 1.90
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.361, 74.361, 126.462, 90, 90, 120
R / Rfree (%)	19.5 / 25.1

The structure of Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin (pdb code 7nug). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin, PDB code: 7nug:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:15.8 occ:1.00 OD2 A:ASP108 2.1 15.4 1.0 O A:ILE120 2.2 16.2 1.0 O10 A:USE212 2.2 16.8 1.0 OE2 A:GLU119 2.2 18.0 1.0 O11 A:USE212 2.2 17.8 1.0 NE2 A:HIS41 2.3 13.8 1.0 C4 A:USE212 2.9 18.0 1.0 C3 A:USE212 2.9 18.8 1.0 CG A:ASP108 3.0 16.0 1.0 CE1 A:HIS41 3.1 14.5 1.0 CD A:GLU119 3.2 19.2 1.0 OD1 A:ASP108 3.3 13.1 1.0 C A:ILE120 3.3 18.7 1.0 CD2 A:HIS41 3.3 13.6 1.0 N A:ILE120 3.7 17.5 1.0 MN A:MN202 3.8 21.6 0.6 MG A:MG203 3.8 19.6 0.6 OE1 A:GLU119 3.8 19.3 1.0 NZ A:LYS134 3.9 24.8 1.0 CA A:ILE120 4.0 17.8 1.0 O A:HOH324 4.2 18.7 1.0 ND1 A:HIS41 4.2 12.4 1.0 C5 A:USE212 4.2 19.3 1.0 C2 A:USE212 4.3 20.4 1.0 CG A:GLU119 4.3 19.3 1.0 O A:HOH339 4.3 11.7 1.0 CB A:ILE120 4.4 18.7 1.0 O A:HOH338 4.4 38.6 1.0 CG A:HIS41 4.4 13.4 1.0 CB A:ASP108 4.4 15.6 1.0 N A:GLY121 4.4 17.9 1.0 CE A:LYS134 4.5 27.8 1.0 C A:GLU119 4.7 18.6 1.0 OE1 A:GLU80 4.7 19.5 1.0 CA A:GLY121 4.8 17.6 1.0

Manganese binding site 2 out of 2 in the Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Orientin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:21.6 occ:0.57 MG A:MG203 0.5 19.6 0.6 O A:HOH324 2.2 18.7 1.0 OD1 A:ASP108 2.2 13.1 1.0 O A:HOH431 2.2 18.1 1.0 OE1 A:GLU80 2.3 19.5 1.0 O10 A:USE212 2.3 16.8 1.0 O A:HOH400 2.4 15.2 1.0 CG A:ASP108 3.2 16.0 1.0 C4 A:USE212 3.4 18.0 1.0 CD A:GLU80 3.4 18.5 1.0 C5 A:USE212 3.7 19.3 1.0 OD2 A:ASP108 3.7 15.4 1.0 MN A:MN201 3.8 15.8 1.0 O A:HOH373 4.1 19.4 1.0 CE1 A:HIS41 4.1 14.5 1.0 O A:HOH371 4.1 24.3 1.0 O A:LEU106 4.1 18.2 1.0 O A:HOH338 4.2 38.6 1.0 OE1 A:GLU119 4.2 19.3 1.0 CG A:GLU80 4.2 18.2 1.0 OE2 A:GLU80 4.3 20.1 1.0 O A:PRO107 4.3 18.4 1.0 OE2 A:GLU119 4.3 18.0 1.0 O A:HOH470 4.4 20.1 1.0 C A:PRO107 4.4 17.0 1.0 CB A:ASP108 4.4 15.6 1.0 CB A:GLU80 4.4 18.3 1.0 CA A:ASP108 4.4 16.9 1.0 N A:ASP108 4.5 16.8 1.0 C3 A:USE212 4.6 18.8 1.0 NE2 A:HIS41 4.6 13.8 1.0 CD A:GLU119 4.7 19.2 1.0 CA A:GLU80 5.0 17.7 1.0 O11 A:USE212 5.0 17.8 1.0

R.Reiberger, K.Radilova, M.Kral, V.Zima, P.Majer, J.Brynda, M.Dracinsky, J.Konvalinka, M.Kozisek, A.Machara. Synthesis and in Vitro Evaluation of C-7 and C-8 Luteolin Derivatives As Influenza Endonuclease Inhibitors Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22147735