Manganese in PDB 8djv: The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide, PDB code: 8djv 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)	37.23 / 2.08
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.465, 74.465, 120.259, 90, 90, 120
R / Rfree (%)	26.3 / 29.1

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Viral Polymerase in Complex with 6-Bromo-3-Hydroxy-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide 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-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide (pdb code 8djv). 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-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide, PDB code: 8djv:
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-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide


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-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:35.4 occ:1.00 O14 A:U3U303 2.0 33.2 1.0 O01 A:U3U303 2.1 32.6 1.0 OE2 A:GLU119 2.1 29.2 1.0 O A:ILE120 2.2 32.7 1.0 OD2 A:ASP108 2.3 35.1 1.0 NE2 A:HIS41 2.5 36.8 1.0 C13 A:U3U303 2.8 34.6 1.0 C02 A:U3U303 2.8 33.6 1.0 CG A:ASP108 3.1 33.1 1.0 CD A:GLU119 3.1 31.9 1.0 OD1 A:ASP108 3.2 29.1 1.0 CE1 A:HIS41 3.3 35.6 1.0 C A:ILE120 3.3 33.0 1.0 CD2 A:HIS41 3.5 35.3 1.0 OE1 A:GLU119 3.6 34.6 1.0 MN A:MN302 3.7 40.6 1.0 N A:ILE120 3.8 38.6 1.0 NZ A:LYS134 3.9 41.0 1.0 CA A:ILE120 4.0 33.6 1.0 C12 A:U3U303 4.2 38.3 1.0 CE A:LYS134 4.3 34.8 1.0 CG A:GLU119 4.3 40.5 1.0 O A:HOH412 4.4 31.9 1.0 C03 A:U3U303 4.4 42.7 1.0 CB A:ILE120 4.4 38.6 1.0 ND1 A:HIS41 4.4 41.2 1.0 N A:GLY121 4.4 35.7 1.0 CG A:HIS41 4.5 37.7 1.0 CB A:ASP108 4.6 32.5 1.0 C A:GLU119 4.6 35.9 1.0 H121 A:U3U303 4.7 46.0 1.0 CA A:GLY121 4.7 34.1 1.0 OE2 A:GLU80 4.9 33.5 1.0 O08 A:U3U303 4.9 35.7 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 6-Bromo-3-Hydroxy-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide


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-N-Methoxy-4-Oxo-1,4- Dihydropyridine-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:40.6 occ:1.00 O08 A:U3U303 1.8 35.7 1.0 O01 A:U3U303 2.0 32.6 1.0 OD1 A:ASP108 2.2 29.1 1.0 O A:HOH430 2.3 37.8 1.0 OE2 A:GLU80 2.4 33.5 1.0 C04 A:U3U303 2.8 37.8 1.0 C02 A:U3U303 3.0 33.6 1.0 C03 A:U3U303 3.3 42.7 1.0 CG A:ASP108 3.4 33.1 1.0 CD A:GLU80 3.4 38.5 1.0 MN A:MN301 3.7 35.4 1.0 CE1 A:HIS41 3.9 35.6 1.0 OD2 A:ASP108 3.9 35.1 1.0 N05 A:U3U303 4.1 50.1 1.0 OE1 A:GLU119 4.1 34.6 1.0 OE1 A:GLU80 4.1 37.1 1.0 CG A:GLU80 4.2 36.5 1.0 C13 A:U3U303 4.3 34.6 1.0 O A:LEU106 4.3 41.0 1.0 O A:HOH446 4.4 47.7 1.0 CB A:GLU80 4.4 38.8 1.0 NE2 A:HIS41 4.4 36.8 1.0 O A:PRO107 4.4 35.5 1.0 OE2 A:GLU119 4.4 29.2 1.0 C A:PRO107 4.5 33.1 1.0 O06 A:U3U303 4.5 54.5 1.0 CB A:ASP108 4.5 32.5 1.0 CA A:ASP108 4.6 38.9 1.0 O14 A:U3U303 4.7 33.2 1.0 N A:ASP108 4.7 33.3 1.0 CD A:GLU119 4.7 31.9 1.0 N09 A:U3U303 4.8 40.2 1.0 H051 A:U3U303 4.9 60.1 1.0 O A:HOH437 5.0 33.5 1.0 ND1 A:HIS41 5.0 41.2 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