Manganese in PDB 8dhn: The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One, PDB code: 8dhn was solved by A.J.Kohlbrand, R.W.Stokes, J.Karges, H.Seo, B.Sankaran, S.M.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.98 / 2.40
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.034, 75.034, 121.24, 90, 90, 120
R / Rfree (%)	20.1 / 25.6

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Manganese atom in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One (pdb code 8dhn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One, PDB code: 8dhn:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:41.1 occ:1.00 O15 A:T6U201 2.1 50.6 1.0 O A:ILE120 2.1 37.1 1.0 OE2 A:GLU119 2.2 42.0 1.0 O01 A:T6U201 2.2 39.6 1.0 NE2 A:HIS41 2.3 46.8 1.0 OD2 A:ASP108 2.3 36.8 1.0 C14 A:T6U201 2.8 46.0 1.0 C02 A:T6U201 2.9 41.9 1.0 CE1 A:HIS41 3.0 38.2 1.0 CG A:ASP108 3.1 36.3 1.0 OD1 A:ASP108 3.1 40.9 1.0 CD A:GLU119 3.3 43.7 1.0 C A:ILE120 3.3 36.2 1.0 CD2 A:HIS41 3.4 38.6 1.0 OE1 A:GLU119 3.8 42.0 1.0 N A:ILE120 3.8 40.7 1.0 MN A:MN203 3.9 57.2 1.0 CA A:ILE120 4.0 48.4 1.0 ND1 A:HIS41 4.1 46.4 1.0 O A:HOH304 4.1 35.0 1.0 O A:HOH313 4.2 35.3 1.0 C13 A:T6U201 4.3 53.1 1.0 CG A:HIS41 4.3 38.2 1.0 N A:GLY121 4.3 32.2 1.0 CG A:GLU119 4.4 42.2 1.0 C03 A:T6U201 4.4 52.3 1.0 CB A:ASP108 4.4 33.9 1.0 NZ A:LYS134 4.4 50.8 1.0 CB A:ILE120 4.5 45.0 1.0 CE A:LYS134 4.5 37.8 1.0 CA A:GLY121 4.6 30.4 1.0 C A:GLU119 4.7 36.3 1.0 H131 A:T6U201 4.7 64.7 1.0 OE1 A:GLU80 4.9 42.5 1.0

Manganese binding site 2 out of 2 in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-2-(5-Methyl-1,2,4- Oxadiazol-3-Yl)Pyridin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:57.2 occ:1.00 O01 A:T6U201 2.2 39.6 1.0 N05 A:T6U201 2.2 72.4 1.0 O A:HOH334 2.2 44.0 1.0 OE1 A:GLU80 2.3 42.5 1.0 OD1 A:ASP108 2.3 40.9 1.0 O A:HOH304 2.5 35.0 1.0 O06 A:T6U201 3.0 86.1 1.0 C04 A:T6U201 3.0 63.3 1.0 CG A:ASP108 3.1 36.3 1.0 C02 A:T6U201 3.2 41.9 1.0 CD A:GLU80 3.4 54.2 1.0 OD2 A:ASP108 3.5 36.8 1.0 C03 A:T6U201 3.6 52.3 1.0 CE1 A:HIS41 3.9 38.2 1.0 MN A:MN202 3.9 41.1 1.0 C07 A:T6U201 4.0 73.2 1.0 N09 A:T6U201 4.0 80.3 1.0 O A:PRO107 4.1 34.1 1.0 O A:LEU106 4.1 49.1 1.0 OE2 A:GLU80 4.2 46.6 1.0 CB A:ASP108 4.2 33.9 1.0 CB A:GLU80 4.3 39.9 1.0 CA A:ASP108 4.3 41.1 1.0 CG A:GLU80 4.3 45.3 1.0 C A:PRO107 4.3 39.3 1.0 OE1 A:GLU119 4.3 42.0 1.0 N A:ASP108 4.5 34.8 1.0 C14 A:T6U201 4.5 46.0 1.0 NE2 A:HIS41 4.6 46.8 1.0 OE2 A:GLU119 4.7 42.0 1.0 O15 A:T6U201 4.9 50.6 1.0 ND1 A:HIS41 4.9 46.4 1.0 O A:HOH341 4.9 59.1 1.0 CD A:GLU119 5.0 43.7 1.0 CA A:GLU80 5.0 40.1 1.0

R.W.Stokes, A.J.Kohlbrand, H.Seo, B.Sankaran, J.Karges, S.M.Cohen. Carboxylic Acid Isostere Derivatives of Hydroxypyridinones As Core Scaffolds For Influenza Endonuclease Inhibitors Acs Med.Chem.Lett. 2022.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.2C00434