Manganese in PDB 5wa7: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9B (Sri-30101)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9B (Sri-30101), PDB code: 5wa7 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)	40.45 / 2.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.298, 90.298, 135.708, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 24.9

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9B (Sri-30101) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9B (Sri-30101) (pdb code 5wa7). 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 9B (Sri-30101), PDB code: 5wa7:
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 9B (Sri-30101)


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 9B (Sri-30101) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:87.0 occ:1.00 OE1 A:GLU119 2.1 96.8 1.0 OD1 A:ASP108 2.1 77.0 1.0 O A:ILE120 2.3 80.9 1.0 NE2 A:HIS41 2.3 75.4 1.0 O1 A:KU4204 2.4 0.7 1.0 O2 A:KU4204 2.4 0.7 1.0 CD A:GLU119 2.9 90.8 1.0 CG A:ASP108 3.0 78.8 1.0 OE2 A:GLU119 3.1 90.7 1.0 C1 A:KU4204 3.1 0.6 1.0 CE1 A:HIS41 3.1 68.2 1.0 OD2 A:ASP108 3.2 74.1 1.0 C2 A:KU4204 3.2 0.6 1.0 C A:ILE120 3.4 80.0 1.0 CD2 A:HIS41 3.4 70.2 1.0 N A:ILE120 3.6 73.9 1.0 O A:HOH301 3.7 75.2 1.0 CA A:ILE120 4.0 80.6 1.0 MN A:MN202 4.0 0.1 1.0 CG A:GLU119 4.3 87.8 1.0 ND1 A:HIS41 4.3 67.8 1.0 C A:GLU119 4.4 82.7 1.0 CB A:ASP108 4.4 75.4 1.0 N4 A:KU4204 4.5 0.7 1.0 CG A:HIS41 4.5 74.7 1.0 N A:GLY121 4.5 85.8 1.0 C3 A:KU4204 4.5 0.1 1.0 O A:HOH305 4.6 75.0 1.0 CB A:ILE120 4.6 84.8 1.0 CA A:GLU119 4.7 80.0 1.0 CA A:GLY121 4.8 79.9 1.0 O4 A:KU4204 4.9 0.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9B (Sri-30101)


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 9B (Sri-30101) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:0.1 occ:1.00 O4 A:KU4204 2.2 0.8 1.0 OD2 A:ASP108 2.4 74.1 1.0 O A:HOH301 2.5 75.2 1.0 O2 A:KU4204 2.5 0.7 1.0 O A:HOH304 2.5 93.9 1.0 OE1 A:GLU80 2.6 92.4 1.0 C4 A:KU4204 3.3 0.5 1.0 CG A:ASP108 3.6 78.8 1.0 C2 A:KU4204 3.6 0.6 1.0 CD A:GLU80 3.6 86.2 1.0 CE1 A:HIS41 3.8 68.2 1.0 C3 A:KU4204 4.0 0.1 1.0 MN A:MN201 4.0 87.0 1.0 OD1 A:ASP108 4.2 77.0 1.0 OE2 A:GLU80 4.3 95.7 1.0 O A:LEU106 4.3 75.9 1.0 O A:PRO107 4.4 80.2 1.0 NE2 A:HIS41 4.4 75.4 1.0 N1 A:KU4204 4.5 0.4 1.0 CB A:GLU80 4.5 72.5 1.0 OE2 A:GLU119 4.5 90.7 1.0 CG A:GLU80 4.6 74.5 1.0 C A:PRO107 4.6 79.7 1.0 CB A:ASP108 4.7 75.4 1.0 ND1 A:HIS41 4.7 67.8 1.0 CA A:ASP108 4.7 78.0 1.0 C5 A:KU4204 4.8 0.9 1.0 C1 A:KU4204 4.8 0.6 1.0 N A:ASP108 4.8 74.4 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