Manganese in PDB 8ddb: The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 4-(Benzyloxy)-6-Bromo-3-Hydroxypicolinic Acid

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 4-(Benzyloxy)-6-Bromo-3-Hydroxypicolinic Acid, PDB code: 8ddb 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)	58.02 / 2.15
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	76.228, 76.228, 121.608, 90, 90, 120
R / Rfree (%)	19.2 / 24.1

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 4-(Benzyloxy)-6-Bromo-3-Hydroxypicolinic Acid 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-3-Hydroxypicolinic Acid (pdb code 8ddb). 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-3-Hydroxypicolinic Acid, PDB code: 8ddb:
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-3-Hydroxypicolinic Acid


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-3-Hydroxypicolinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:50.1 occ:1.00 OD2 A:ASP108 2.1 47.5 1.0 O12 A:R6X304 2.1 53.7 1.0 O01 A:R6X304 2.2 62.2 1.0 O A:ILE120 2.2 47.3 1.0 OE2 A:GLU119 2.3 49.8 1.0 NE2 A:HIS41 2.3 51.0 1.0 C11 A:R6X304 2.8 61.5 1.0 C02 A:R6X304 2.9 54.3 1.0 CG A:ASP108 3.0 48.0 1.0 CE1 A:HIS41 3.0 55.1 1.0 OD1 A:ASP108 3.2 51.4 1.0 CD A:GLU119 3.2 57.1 1.0 C A:ILE120 3.3 49.4 1.0 CD2 A:HIS41 3.4 55.5 1.0 OE1 A:GLU119 3.7 56.5 1.0 N A:ILE120 3.7 43.6 1.0 MN A:MN302 3.8 71.4 1.0 NZ A:LYS134 3.9 57.1 1.0 CA A:ILE120 4.0 47.9 1.0 O A:HOH404 4.1 49.5 1.0 ND1 A:HIS41 4.2 52.4 1.0 C10 A:R6X304 4.3 62.9 1.0 CB A:ILE120 4.3 55.5 1.0 CB A:ASP108 4.4 51.8 1.0 C03 A:R6X304 4.4 63.6 1.0 CG A:HIS41 4.4 50.8 1.0 CG A:GLU119 4.4 51.2 1.0 O A:HOH432 4.4 48.9 1.0 N A:GLY121 4.4 49.4 1.0 CE A:LYS134 4.6 60.2 1.0 C A:GLU119 4.7 48.0 1.0 CA A:GLY121 4.7 43.7 1.0 H101 A:R6X304 4.7 75.6 1.0 O05 A:R6X304 4.9 74.8 1.0 OE2 A:GLU80 4.9 57.7 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-3-Hydroxypicolinic Acid


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-3-Hydroxypicolinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:71.4 occ:1.00 O05 A:R6X304 2.0 74.8 1.0 O01 A:R6X304 2.1 62.2 1.0 OD1 A:ASP108 2.2 51.4 1.0 OE2 A:GLU80 2.3 57.7 1.0 O A:HOH436 2.3 58.0 1.0 O A:HOH404 2.5 49.5 1.0 C04 A:R6X304 2.9 68.9 1.0 C02 A:R6X304 3.1 54.3 1.0 CD A:GLU80 3.2 63.6 1.0 CG A:ASP108 3.3 48.0 1.0 C03 A:R6X304 3.5 63.6 1.0 MN A:MN301 3.8 50.1 1.0 OD2 A:ASP108 3.8 47.5 1.0 CE1 A:HIS41 3.9 55.1 1.0 OE1 A:GLU80 3.9 75.6 1.0 O06 A:R6X304 4.0 76.9 1.0 CG A:GLU80 4.0 58.5 1.0 O A:PRO107 4.1 53.8 1.0 CB A:GLU80 4.2 52.4 1.0 O A:LEU106 4.2 57.3 1.0 C A:PRO107 4.4 48.5 1.0 OE1 A:GLU119 4.4 56.5 1.0 CB A:ASP108 4.4 51.8 1.0 CA A:ASP108 4.4 44.7 1.0 C11 A:R6X304 4.5 61.5 1.0 NE2 A:HIS41 4.5 51.0 1.0 N A:ASP108 4.6 49.1 1.0 OE2 A:GLU119 4.7 49.8 1.0 O12 A:R6X304 4.8 53.7 1.0 ND1 A:HIS41 4.8 52.4 1.0 N07 A:R6X304 4.9 74.5 1.0 CA A:GLU80 5.0 52.5 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