Manganese in PDB 8djy: The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-4(1H)-One

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-4(1H)-One, PDB code: 8djy 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)	44.29 / 2.50
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.807, 75.807, 119.978, 90, 90, 120
R / Rfree (%)	21.2 / 28.6

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-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-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-4(1H)-One (pdb code 8djy). 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-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-4(1H)-One, PDB code: 8djy:
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-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-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-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:55.2 occ:1.00 O14 A:U3L201 2.0 53.9 1.0 OD2 A:ASP108 2.2 51.7 1.0 O A:ILE120 2.2 51.0 1.0 O01 A:U3L201 2.2 55.2 1.0 NE2 A:HIS41 2.3 52.0 1.0 OE2 A:GLU119 2.3 52.0 1.0 C13 A:U3L201 2.8 56.2 1.0 C02 A:U3L201 2.9 56.8 1.0 CE1 A:HIS41 2.9 50.7 1.0 CG A:ASP108 3.1 51.0 1.0 CD A:GLU119 3.2 53.7 1.0 C A:ILE120 3.3 48.7 1.0 OD1 A:ASP108 3.3 52.4 1.0 CD2 A:HIS41 3.5 50.0 1.0 N A:ILE120 3.6 48.8 1.0 OE1 A:GLU119 3.7 54.7 1.0 CA A:ILE120 3.9 49.0 1.0 MN A:MN203 3.9 60.3 1.0 NZ A:LYS134 3.9 55.3 1.0 ND1 A:HIS41 4.1 50.1 1.0 O A:HOH320 4.2 51.0 1.0 C12 A:U3L201 4.2 61.8 1.0 O A:HOH302 4.2 52.3 1.0 CB A:ILE120 4.2 47.4 1.0 CG A:GLU119 4.2 52.0 1.0 N A:GLY121 4.3 46.4 1.0 C03 A:U3L201 4.4 61.2 1.0 CG A:HIS41 4.4 49.0 1.0 CB A:ASP108 4.4 50.6 1.0 C A:GLU119 4.6 50.8 1.0 CE A:LYS134 4.6 49.9 1.0 H121 A:U3L201 4.6 74.3 1.0 CA A:GLY121 4.7 46.8 1.0 CA A:GLU119 4.9 50.7 1.0 OE1 A:GLU80 5.0 54.2 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-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-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-2-(4,5-Dihydro-1H-Imidazol-2-Yl)- 3-Hydroxypyridin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:60.3 occ:1.00 N05 A:U3L201 1.8 58.8 1.0 O01 A:U3L201 2.0 55.2 1.0 OD1 A:ASP108 2.2 52.4 1.0 OE1 A:GLU80 2.4 54.2 1.0 O A:HOH347 2.6 52.7 1.0 O A:HOH302 2.6 52.3 1.0 C04 A:U3L201 2.9 61.1 1.0 C06 A:U3L201 2.9 63.0 1.0 H062 A:U3L201 3.0 75.7 1.0 C02 A:U3L201 3.1 56.8 1.0 CG A:ASP108 3.2 51.0 1.0 H061 A:U3L201 3.3 75.7 1.0 C03 A:U3L201 3.4 61.2 1.0 CD A:GLU80 3.5 53.4 1.0 OD2 A:ASP108 3.7 51.7 1.0 MN A:MN202 3.9 55.2 1.0 CE1 A:HIS41 3.9 50.7 1.0 N08 A:U3L201 4.1 68.1 1.0 O A:LEU106 4.1 52.3 1.0 C07 A:U3L201 4.1 74.8 1.0 O A:PRO107 4.2 49.9 1.0 OE2 A:GLU80 4.2 53.7 1.0 CB A:GLU80 4.3 52.3 1.0 C A:PRO107 4.3 51.1 1.0 CA A:ASP108 4.3 50.7 1.0 CG A:GLU80 4.3 51.5 1.0 CB A:ASP108 4.3 50.6 1.0 OE1 A:GLU119 4.3 54.7 1.0 N A:ASP108 4.4 50.8 1.0 C13 A:U3L201 4.4 56.2 1.0 H072 A:U3L201 4.6 89.9 1.0 OE2 A:GLU119 4.6 52.0 1.0 NE2 A:HIS41 4.7 52.0 1.0 H071 A:U3L201 4.8 89.9 1.0 O14 A:U3L201 4.8 53.9 1.0 ND1 A:HIS41 4.8 50.1 1.0 CA A:GLU80 4.9 51.6 1.0 N09 A:U3L201 4.9 66.9 1.0 CD A:GLU119 4.9 53.7 1.0 H081 A:U3L201 5.0 81.8 1.0 CA A:PRO107 5.0 51.2 1.0 C A:LEU106 5.0 51.5 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