Manganese in PDB 8t5v: Influenza Pa-N Endonuclease A36V Mutant with Baloxavir

The structure of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir, PDB code: 8t5v was solved by A.J.Kohlbrand, S.M.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.71 / 1.79
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.724, 74.724, 121.619, 90, 90, 120
R / Rfree (%)	23.2 / 28.4

The structure of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Manganese atom in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir (pdb code 8t5v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir, PDB code: 8t5v:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:41.4 occ:1.00 O1 A:E4Z303 2.0 47.3 1.0 OD2 A:ASP108 2.1 44.2 1.0 O A:ILE120 2.2 43.6 1.0 OE2 A:GLU119 2.2 46.3 1.0 NE2 A:HIS41 2.3 40.2 1.0 O2 A:E4Z303 2.5 45.3 1.0 C1 A:E4Z303 2.9 44.0 1.0 CG A:ASP108 3.0 43.5 1.0 C5 A:E4Z303 3.1 44.7 1.0 CD2 A:HIS41 3.1 39.7 1.0 OD1 A:ASP108 3.2 48.0 1.0 CD A:GLU119 3.2 43.7 1.0 C A:ILE120 3.3 42.8 1.0 CE1 A:HIS41 3.4 42.2 1.0 N A:ILE120 3.8 43.5 1.0 MN A:MN302 3.8 45.7 1.0 OE1 A:GLU119 3.8 43.3 1.0 O A:HOH405 4.0 41.4 1.0 CA A:ILE120 4.0 40.9 1.0 C2 A:E4Z303 4.1 48.5 1.0 NZ A:LYS134 4.2 56.2 1.0 CG A:GLU119 4.2 47.9 1.0 CB A:ILE120 4.2 43.6 1.0 CG A:HIS41 4.3 44.6 1.0 O A:HOH417 4.3 38.1 1.0 ND1 A:HIS41 4.4 41.4 1.0 CB A:ASP108 4.4 45.5 1.0 N A:GLY121 4.4 41.2 1.0 C4 A:E4Z303 4.5 46.2 1.0 H1 A:E4Z303 4.5 58.7 1.0 CE A:LYS134 4.6 49.4 1.0 CA A:GLY121 4.7 38.4 1.0 C A:GLU119 4.7 42.8 1.0 OE2 A:GLU80 4.8 55.5 1.0 CG2 A:ILE120 4.9 39.5 1.0

Manganese binding site 2 out of 2 in the Influenza Pa-N Endonuclease A36V Mutant with Baloxavir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza Pa-N Endonuclease A36V Mutant with Baloxavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:45.7 occ:1.00 O2 A:E4Z303 2.0 45.3 1.0 O A:HOH405 2.1 41.4 1.0 OE2 A:GLU80 2.2 55.5 1.0 O A:HOH408 2.2 39.1 1.0 OD1 A:ASP108 2.4 48.0 1.0 O3 A:E4Z303 2.4 40.3 1.0 CG A:ASP108 3.2 43.5 1.0 C5 A:E4Z303 3.2 44.7 1.0 C6 A:E4Z303 3.3 46.4 1.0 CD A:GLU80 3.4 57.5 1.0 OD2 A:ASP108 3.6 44.2 1.0 MN A:MN301 3.8 41.4 1.0 C4 A:E4Z303 3.8 46.2 1.0 CE1 A:HIS41 3.9 42.2 1.0 OE1 A:GLU80 4.0 57.2 1.0 NE2 A:HIS41 4.1 40.2 1.0 O A:PRO107 4.2 44.8 1.0 OE1 A:GLU119 4.3 43.3 1.0 CG A:GLU80 4.3 56.2 1.0 OE2 A:GLU119 4.3 46.3 1.0 O A:LEU106 4.3 48.4 1.0 C1 A:E4Z303 4.4 44.0 1.0 CB A:ASP108 4.4 45.5 1.0 C A:PRO107 4.5 41.5 1.0 CB A:GLU80 4.5 49.6 1.0 CA A:ASP108 4.5 45.4 1.0 H17 A:E4Z303 4.6 61.1 1.0 O A:HOH442 4.6 50.1 1.0 H9 A:E4Z303 4.6 54.5 1.0 O1 A:E4Z303 4.6 47.3 1.0 N3 A:E4Z303 4.7 50.5 1.0 N A:ASP108 4.7 44.8 1.0 CD A:GLU119 4.7 43.7 1.0

A.J.Kohlbrand, R.W.Stokes, B.Sankaran, S.M.Cohen. Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants. Biochemistry V. 63 264 2024.
ISSN: ISSN 0006-2960
PubMed: 38190441
DOI: 10.1021/ACS.BIOCHEM.3C00536