Manganese in PDB 8dde: The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol, PDB code: 8dde 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)	57.81 / 2.22
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.979, 75.979, 121.005, 90, 90, 120
R / Rfree (%)	18.8 / 24.4

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol 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 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol (pdb code 8dde). 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 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol, PDB code: 8dde:
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 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol


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 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:46.0 occ:1.00 O01 A:R7C201 1.9 50.0 1.0 O14 A:R7C201 2.2 52.1 1.0 OD2 A:ASP108 2.2 45.3 1.0 NE2 A:HIS41 2.2 54.2 1.0 O A:ILE120 2.2 42.7 1.0 OE2 A:GLU119 2.2 49.6 1.0 C02 A:R7C201 2.7 55.4 1.0 C13 A:R7C201 2.8 63.4 1.0 CE1 A:HIS41 2.9 49.3 1.0 CG A:ASP108 3.1 48.0 1.0 OD1 A:ASP108 3.3 50.4 1.0 CD A:GLU119 3.3 54.7 1.0 CD2 A:HIS41 3.3 46.5 1.0 C A:ILE120 3.4 49.2 1.0 MN A:MN203 3.7 61.7 1.0 N A:ILE120 3.8 45.1 1.0 OE1 A:GLU119 3.8 57.9 1.0 CA A:ILE120 4.0 45.0 1.0 NZ A:LYS134 4.1 63.7 1.0 ND1 A:HIS41 4.1 48.7 1.0 C03 A:R7C201 4.2 62.4 1.0 O A:HOH302 4.2 44.6 1.0 C12 A:R7C201 4.2 67.0 1.0 CB A:ILE120 4.3 57.1 1.0 O A:HOH306 4.3 44.7 1.0 CG A:HIS41 4.3 49.9 1.0 CG A:GLU119 4.4 50.6 1.0 N A:GLY121 4.5 41.3 1.0 CB A:ASP108 4.5 42.4 1.0 C A:GLU119 4.7 44.3 1.0 CA A:GLY121 4.8 39.3 1.0 H121 A:R7C201 4.8 80.5 1.0 OE2 A:GLU80 4.8 48.0 1.0 N08 A:R7C201 4.8 65.7 1.0 CG2 A:ILE120 4.9 54.8 1.0 C04 A:R7C201 5.0 64.0 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 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol


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 4-(Benzyloxy)-6-Bromo-2-(1H-Tetrazol-5-Yl) Yridine-3-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:61.7 occ:1.00 N08 A:R7C201 1.9 65.7 1.0 OD1 A:ASP108 2.0 50.4 1.0 OE2 A:GLU80 2.2 48.0 1.0 O01 A:R7C201 2.2 50.0 1.0 O A:HOH319 2.3 52.4 1.0 O A:HOH302 2.5 44.6 1.0 N07 A:R7C201 2.8 75.2 1.0 C04 A:R7C201 2.8 64.0 1.0 CG A:ASP108 3.1 48.0 1.0 C02 A:R7C201 3.2 55.4 1.0 CD A:GLU80 3.2 61.3 1.0 C03 A:R7C201 3.4 62.4 1.0 OD2 A:ASP108 3.6 45.3 1.0 MN A:MN202 3.7 46.0 1.0 CE1 A:HIS41 3.9 49.3 1.0 N06 A:R7C201 3.9 88.6 1.0 OE1 A:GLU80 3.9 73.1 1.0 N05 A:R7C201 3.9 69.0 1.0 CG A:GLU80 4.0 52.6 1.0 O A:PRO107 4.2 53.5 1.0 CB A:GLU80 4.2 49.9 1.0 O A:HOH311 4.2 68.7 1.0 CB A:ASP108 4.3 42.4 1.0 O A:LEU106 4.3 58.0 1.0 OE1 A:GLU119 4.3 57.9 1.0 CA A:ASP108 4.4 45.5 1.0 C A:PRO107 4.4 51.3 1.0 NE2 A:HIS41 4.5 54.2 1.0 OE2 A:GLU119 4.5 49.6 1.0 C13 A:R7C201 4.6 63.4 1.0 N A:ASP108 4.6 46.0 1.0 N09 A:R7C201 4.8 69.2 1.0 ND1 A:HIS41 4.8 48.7 1.0 CD A:GLU119 4.9 54.7 1.0 CA A:GLU80 4.9 51.3 1.0 O14 A:R7C201 5.0 52.1 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