Manganese in PDB 5wdn: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6D (Sri-29680)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6D (Sri-29680), PDB code: 5wdn 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)	34.99 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.168, 60.168, 94.443, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 23.2

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6D (Sri-29680) (pdb code 5wdn). 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 6D (Sri-29680), PDB code: 5wdn:
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 6D (Sri-29680)


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 6D (Sri-29680) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:45.4 occ:1.00 OD2 A:ASP108 2.0 43.6 1.0 O4 A:G1K303 2.1 45.9 1.0 O A:ILE120 2.2 43.0 1.0 OE2 A:GLU119 2.2 46.5 1.0 O2 A:G1K303 2.2 44.0 1.0 NE2 A:HIS41 2.3 47.8 1.0 CG A:ASP108 3.0 43.5 1.0 CE1 A:HIS41 3.1 47.8 1.0 CD A:GLU119 3.2 46.5 1.0 C4 A:G1K303 3.2 50.3 1.0 C2 A:G1K303 3.3 47.3 1.0 OD1 A:ASP108 3.3 43.8 1.0 C A:ILE120 3.3 43.2 1.0 CD2 A:HIS41 3.4 47.2 1.0 C3 A:G1K303 3.7 50.7 1.0 MN A:MN302 3.7 43.9 1.0 OE1 A:GLU119 3.7 45.9 1.0 N A:ILE120 3.7 44.4 1.0 O A:HOH404 3.9 41.5 1.0 CA A:ILE120 4.0 43.7 1.0 ND1 A:HIS41 4.2 48.5 1.0 O3 A:G1K303 4.3 53.8 1.0 CB A:ILE120 4.3 43.8 1.0 CB A:ASP108 4.3 43.0 1.0 CG A:GLU119 4.4 47.3 1.0 CG A:HIS41 4.4 47.5 1.0 O A:HOH414 4.4 43.9 1.0 N A:GLY121 4.4 45.6 1.0 C1 A:G1K303 4.4 50.1 1.0 C A:GLU119 4.7 44.3 1.0 CA A:GLY121 4.7 45.5 1.0 CE A:LYS134 4.8 63.4 1.0 O1 A:G1K303 4.8 47.5 1.0 OE2 A:GLU80 4.8 44.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6D (Sri-29680)


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 6D (Sri-29680) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:43.9 occ:1.00 O1 A:G1K303 2.0 47.5 1.0 OD1 A:ASP108 2.1 43.8 1.0 OE2 A:GLU80 2.1 44.1 1.0 O A:HOH404 2.1 41.5 1.0 O2 A:G1K303 2.2 44.0 1.0 O A:HOH417 2.2 38.1 1.0 C1 A:G1K303 2.7 50.1 1.0 C2 A:G1K303 2.9 47.3 1.0 CG A:ASP108 3.0 43.5 1.0 CD A:GLU80 3.2 43.7 1.0 OD2 A:ASP108 3.5 43.6 1.0 MN A:MN301 3.7 45.4 1.0 CE1 A:HIS41 3.9 47.8 1.0 CG A:GLU80 4.0 44.6 1.0 N3 A:G1K303 4.1 52.8 1.0 O A:HOH424 4.1 53.1 1.0 OE1 A:GLU80 4.1 45.0 1.0 CB A:ASP108 4.2 43.0 1.0 CA A:ASP108 4.2 42.4 1.0 O A:PRO107 4.2 42.9 1.0 C3 A:G1K303 4.2 50.7 1.0 O A:LEU106 4.3 43.6 1.0 CB A:GLU80 4.3 44.2 1.0 OE1 A:GLU119 4.3 45.9 1.0 C A:PRO107 4.4 43.1 1.0 N A:ASP108 4.4 42.5 1.0 O A:HOH410 4.4 58.3 1.0 NE2 A:HIS41 4.4 47.8 1.0 OE2 A:GLU119 4.6 46.5 1.0 O4 A:G1K303 4.7 45.9 1.0 CA A:GLU80 4.9 45.0 1.0 ND1 A:HIS41 4.9 48.5 1.0 CD A:GLU119 4.9 46.5 1.0 NH2 A:ARG84 5.0 74.3 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