Magnesium in PDB 8pup: Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Purpurogallin-Like Compound

The structure of Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Purpurogallin-Like Compound, PDB code: 8pup was solved by T.Kotacka, K.Radilova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.02 / 2.00
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.95, 73.95, 126.61, 90, 90, 120
R / Rfree (%)	21.6 / 26.5

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

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Purpurogallin-Like Compound (pdb code 8pup). 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 Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Purpurogallin-Like Compound, PDB code: 8pup:

Magnesium binding site 1 out of 1 in the Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Purpurogallin-Like Compound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Influenza A/California/07/2009(H1N1) Endonuclease in Complex with Purpurogallin-Like Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:33.2 occ:1.00 OD1 A:ASP108 1.9 29.5 1.0 O5 A:H2I208 2.0 38.1 1.0 O6 A:H2I208 2.0 39.5 1.0 OE1 A:GLU80 2.1 31.4 1.0 O A:HOH309 2.1 34.7 1.0 O A:HOH319 2.3 32.0 1.0 C17 A:H2I208 2.9 39.0 1.0 C19 A:H2I208 3.0 35.9 1.0 CG A:ASP108 3.0 35.5 1.0 CD A:GLU80 3.2 36.1 1.0 C18 A:H2I208 3.4 45.7 1.0 MN A:MN201 3.5 41.0 1.0 OD2 A:ASP108 3.6 33.3 1.0 CE1 A:HIS41 3.7 34.3 1.0 CG A:GLU80 4.0 36.2 1.0 O A:HOH329 4.0 36.5 1.0 OE2 A:GLU80 4.0 34.1 1.0 C16 A:H2I208 4.1 45.0 1.0 O4 A:H2I208 4.1 40.0 1.0 CB A:GLU80 4.1 34.2 1.0 O A:PRO107 4.2 32.7 1.0 NE2 A:HIS41 4.2 31.9 1.0 C1 A:H2I208 4.2 40.7 1.0 CB A:ASP108 4.2 36.1 1.0 OE1 A:GLU119 4.3 36.1 1.0 CA A:ASP108 4.4 34.3 1.0 C A:PRO107 4.4 33.0 1.0 O A:LEU106 4.5 33.5 1.0 OE2 A:GLU119 4.5 43.8 1.0 O1 A:H2I208 4.5 43.6 1.0 N A:ASP108 4.6 31.9 1.0 C2 A:EDO206 4.8 71.2 1.0 C4 A:H2I208 4.8 49.8 1.0 CA A:GLU80 4.8 33.6 1.0 CD A:GLU119 4.8 41.8 1.0 ND1 A:HIS41 4.9 30.9 1.0 O A:HOH361 5.0 70.8 1.0

M.Kral, T.Kotacka, R.Reiberger, G.Panyrkova, K.Radilova, Z.Osifova, M.Flieger, J.Konvalinka, P.Majer, M.Kozisek, A.Machara. 3'-Dehydroxypurpurogallin-4-Carboxamides As Influenza A Endonuclease Inhibitors: Synthesis, Structure-Activity Relationship Analysis, and Structural Characterization of Protein Complex. Chemmedchem 00577 2024.
ISSN: ESSN 1860-7187
PubMed: 39400442
DOI: 10.1002/CMDC.202400577