Manganese in PDB 5w7u: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 8F (Sri-29928)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 8F (Sri-29928), PDB code: 5w7u was solved by G.Kumar, S.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.08 / 2.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.746, 90.746, 135.256, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.4

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 8F (Sri-29928) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 8F (Sri-29928) (pdb code 5w7u). 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 in Complex with Inhibitor 8F (Sri-29928), PDB code: 5w7u:
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 in Complex with Inhibitor 8F (Sri-29928)


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 in Complex with Inhibitor 8F (Sri-29928) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:81.1 occ:1.00 O4 A:GY8203 1.9 78.3 1.0 NE2 A:HIS41 2.1 79.8 1.0 O3 A:GY8203 2.2 78.0 1.0 O A:ILE120 2.2 72.9 1.0 OD2 A:ASP108 2.2 79.0 1.0 OE1 A:GLU119 2.6 81.1 1.0 C18 A:GY8203 2.7 79.2 1.0 C17 A:GY8203 2.8 77.2 1.0 CE1 A:HIS41 2.9 75.8 1.0 CG A:ASP108 3.0 79.0 1.0 OE2 A:GLU119 3.1 0.8 1.0 CD A:GLU119 3.1 93.9 1.0 OD1 A:ASP108 3.2 78.0 1.0 CD2 A:HIS41 3.2 76.3 1.0 C A:ILE120 3.4 80.1 1.0 MN A:MN202 3.5 87.9 1.0 N A:ILE120 3.7 72.2 1.0 O A:HOH302 4.0 58.5 1.0 N4 A:GY8203 4.0 89.9 1.0 CA A:ILE120 4.0 78.6 1.0 ND1 A:HIS41 4.0 73.3 1.0 C6 A:GY8203 4.2 85.4 1.0 CG A:HIS41 4.2 80.3 1.0 CB A:ILE120 4.3 82.3 1.0 O A:HOH305 4.4 80.0 1.0 CB A:ASP108 4.4 76.9 1.0 N A:GLY121 4.5 83.6 1.0 CG A:GLU119 4.5 0.1 1.0 C A:GLU119 4.6 81.5 1.0 CE A:LYS134 4.6 1.0 1.0 OE2 A:GLU80 4.6 76.4 1.0 CA A:GLY121 4.8 80.5 1.0 O2 A:GY8203 4.9 87.8 1.0 CA A:GLU119 4.9 81.0 1.0 NZ A:LYS134 5.0 0.3 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 8F (Sri-29928)


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 in Complex with Inhibitor 8F (Sri-29928) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:87.9 occ:1.00 O A:HOH301 1.8 52.5 1.0 O3 A:GY8203 1.8 78.0 1.0 OD1 A:ASP108 2.0 78.0 1.0 OE2 A:GLU80 2.0 76.4 1.0 O2 A:GY8203 2.1 87.8 1.0 O A:HOH302 2.3 58.5 1.0 C17 A:GY8203 2.9 77.2 1.0 C7 A:GY8203 2.9 90.9 1.0 CD A:GLU80 3.1 80.3 1.0 CG A:ASP108 3.1 79.0 1.0 C6 A:GY8203 3.3 85.4 1.0 MN A:MN201 3.5 81.1 1.0 OD2 A:ASP108 3.5 79.0 1.0 CE1 A:HIS41 3.7 75.8 1.0 OE1 A:GLU119 3.8 81.1 1.0 OE1 A:GLU80 3.9 78.0 1.0 CG A:GLU80 3.9 71.8 1.0 N3 A:GY8203 4.1 96.5 1.0 C18 A:GY8203 4.1 79.2 1.0 O A:PRO107 4.2 71.5 1.0 NE2 A:HIS41 4.3 79.8 1.0 CB A:ASP108 4.3 76.9 1.0 CB A:GLU80 4.3 68.7 1.0 O A:LEU106 4.4 73.4 1.0 C A:PRO107 4.4 80.5 1.0 CA A:ASP108 4.5 78.8 1.0 O4 A:GY8203 4.5 78.3 1.0 N A:ASP108 4.6 71.5 1.0 N2 A:GY8203 4.6 91.2 1.0 ND1 A:HIS41 4.7 73.3 1.0 C8 A:GY8203 4.7 94.2 1.0 CD A:GLU119 4.9 93.9 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