Manganese in PDB 5wef: Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770), PDB code: 5wef was solved by G.Kumar, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.48 / 2.00
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.878, 73.878, 127.282, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.7

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770) (pdb code 5wef). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770), PDB code: 5wef:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:46.4 occ:1.00 O08 A:GY6303 2.1 43.2 1.0 NE2 A:HIS41 2.2 38.6 1.0 O05 A:GY6303 2.2 43.0 1.0 OE1 A:GLU119 2.2 55.8 1.0 OD2 A:ASP108 2.2 39.5 1.0 O A:ILE120 2.2 53.3 1.0 C07 A:GY6303 2.8 50.0 1.0 C04 A:GY6303 3.0 48.3 1.0 CG A:ASP108 3.0 41.8 1.0 CE1 A:HIS41 3.0 39.3 1.0 OD1 A:ASP108 3.2 38.3 1.0 CD2 A:HIS41 3.2 43.0 1.0 CD A:GLU119 3.3 54.2 1.0 C A:ILE120 3.4 53.8 1.0 MN A:MN302 3.6 37.1 0.5 N A:ILE120 3.7 47.7 1.0 OE2 A:GLU119 3.7 54.0 1.0 O A:HOH413 4.0 42.7 1.0 CA A:ILE120 4.0 51.0 1.0 ND1 A:HIS41 4.2 39.9 1.0 N09 A:GY6303 4.2 56.4 1.0 CE A:LYS134 4.3 73.1 1.0 CG A:HIS41 4.3 44.1 1.0 C03 A:GY6303 4.3 51.6 1.0 CB A:ILE120 4.3 49.9 1.0 CB A:ASP108 4.5 38.2 1.0 CG A:GLU119 4.5 51.7 1.0 N A:GLY121 4.5 52.5 1.0 OE1 A:GLU80 4.6 39.3 1.0 C A:GLU119 4.7 49.8 1.0 O A:HOH410 4.8 48.3 1.0 CA A:GLY121 4.8 52.0 1.0 O12 A:GY6303 4.9 43.3 1.0 NZ A:LYS134 4.9 72.9 1.0 CG2 A:ILE120 4.9 46.8 1.0 SG A:CYS45 5.0 42.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Influenza Virus Pa Endonuclease (F105S Mutant) in Complex with Inhibitor 7A (Sri-29770) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:37.1 occ:0.45 O05 A:GY6303 2.0 43.0 1.0 O12 A:GY6303 2.0 43.3 1.0 OE1 A:GLU80 2.1 39.3 1.0 OD1 A:ASP108 2.1 38.3 1.0 O A:HOH413 2.1 42.7 1.0 O A:HOH423 2.1 40.2 1.0 C11 A:GY6303 3.0 49.8 1.0 C04 A:GY6303 3.0 48.3 1.0 CD A:GLU80 3.2 41.9 1.0 CG A:ASP108 3.2 41.8 1.0 C03 A:GY6303 3.4 51.6 1.0 MN A:MN301 3.6 46.4 1.0 OD2 A:ASP108 3.8 39.5 1.0 CE1 A:HIS41 3.9 39.3 1.0 CG A:GLU80 4.0 39.6 1.0 OE2 A:GLU80 4.0 44.7 1.0 O A:HOH439 4.1 43.2 1.0 CB A:GLU80 4.2 37.4 1.0 N13 A:GY6303 4.2 54.4 1.0 C07 A:GY6303 4.3 50.0 1.0 OE2 A:GLU119 4.3 54.0 1.0 O A:PRO107 4.3 37.7 1.0 NE2 A:HIS41 4.3 38.6 1.0 CB A:ASP108 4.4 38.2 1.0 C A:PRO107 4.4 38.7 1.0 O A:LEU106 4.4 45.6 1.0 CA A:ASP108 4.4 35.6 1.0 OE1 A:GLU119 4.5 55.8 1.0 N A:ASP108 4.5 36.3 1.0 O08 A:GY6303 4.7 43.2 1.0 C14 A:GY6303 4.7 62.7 1.0 N02 A:GY6303 4.7 56.9 1.0 CD A:GLU119 4.9 54.2 1.0 CA A:GLU80 4.9 41.1 1.0 NA A:NA307 4.9 78.3 1.0 ND1 A:HIS41 5.0 39.9 1.0

D.Beylkin, G.Kumar, W.Zhou, J.Park, T.Jeevan, C.Lagisetti, R.Harfoot, R.J.Webby, S.W.White, T.R.Webb. Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Sci Rep V. 7 17139 2017.
ISSN: ESSN 2045-2322
PubMed: 29215062
DOI: 10.1038/S41598-017-17419-6