Manganese in PDB 5wap: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10I (Sri-30025)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10I (Sri-30025), PDB code: 5wap 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)	33.79 / 2.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.653, 90.653, 135.170, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 24.5

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10I (Sri-30025) 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 10I (Sri-30025) (pdb code 5wap). 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 10I (Sri-30025), PDB code: 5wap:
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 10I (Sri-30025)


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 10I (Sri-30025) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:70.6 occ:1.00 O1 A:KU9204 1.9 69.8 1.0 OD2 A:ASP108 2.1 67.8 1.0 O A:ILE120 2.2 67.8 1.0 OE1 A:GLU119 2.2 79.3 1.0 CE1 A:HIS41 2.3 64.6 1.0 O2 A:KU9204 2.3 67.6 1.0 C1 A:KU9204 2.7 71.8 1.0 NE2 A:HIS41 2.9 65.3 1.0 C2 A:KU9204 3.0 70.1 1.0 CG A:ASP108 3.0 69.6 1.0 CD A:GLU119 3.1 78.6 1.0 OD1 A:ASP108 3.2 67.5 1.0 ND1 A:HIS41 3.3 64.5 1.0 C A:ILE120 3.4 69.7 1.0 OE2 A:GLU119 3.6 75.7 1.0 N A:ILE120 3.7 65.4 1.0 MN A:MN202 3.7 70.0 0.9 O A:HOH302 3.9 65.8 1.0 CA A:ILE120 4.0 65.9 1.0 N4 A:KU9204 4.0 74.8 1.0 CD2 A:HIS41 4.1 61.0 1.0 CG A:GLU119 4.2 76.6 1.0 C3 A:KU9204 4.3 75.4 1.0 CB A:ILE120 4.3 69.9 1.0 CG A:HIS41 4.3 65.0 1.0 CB A:ASP108 4.4 68.5 1.0 O A:HOH307 4.4 87.6 1.0 N A:GLY121 4.5 71.0 1.0 C A:GLU119 4.5 70.9 1.0 OE1 A:GLU80 4.7 67.1 1.0 CA A:GLY121 4.8 69.0 1.0 CA A:GLU119 4.9 71.2 1.0 O3 A:KU9204 4.9 69.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10I (Sri-30025)


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 10I (Sri-30025) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:70.0 occ:0.88 O A:HOH305 2.0 70.9 1.0 O2 A:KU9204 2.0 67.6 1.0 OD1 A:ASP108 2.1 67.5 1.0 O3 A:KU9204 2.1 69.8 1.0 O A:HOH302 2.2 65.8 1.0 OE1 A:GLU80 2.4 67.1 1.0 C4 A:KU9204 3.1 75.1 1.0 C2 A:KU9204 3.1 70.1 1.0 CG A:ASP108 3.2 69.6 1.0 CD A:GLU80 3.2 66.4 1.0 C3 A:KU9204 3.6 75.4 1.0 MN A:MN201 3.7 70.6 1.0 OD2 A:ASP108 3.8 67.8 1.0 OE2 A:GLU80 3.8 67.4 1.0 NE2 A:HIS41 4.0 65.3 1.0 CG A:GLU80 4.2 58.1 1.0 O A:LEU106 4.2 71.2 1.0 CB A:GLU80 4.2 56.3 1.0 O A:PRO107 4.3 66.5 1.0 OE2 A:GLU119 4.3 75.7 1.0 C1 A:KU9204 4.3 71.8 1.0 N1 A:KU9204 4.3 79.3 1.0 CB A:ASP108 4.4 68.5 1.0 CA A:ASP108 4.5 67.9 1.0 C A:PRO107 4.5 72.4 1.0 N A:ASP108 4.6 70.9 1.0 OE1 A:GLU119 4.6 79.3 1.0 CE1 A:HIS41 4.6 64.6 1.0 O1 A:KU9204 4.7 69.8 1.0 C5 A:KU9204 4.8 80.0 1.0 CD A:GLU119 4.9 78.6 1.0 CD2 A:HIS41 4.9 61.0 1.0 C6 A:KU9204 4.9 80.5 1.0 N2 A:KU9204 4.9 81.1 1.0 CA A:GLU80 5.0 59.2 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