Manganese in PDB 5wfm: Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024), PDB code: 5wfm 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)	38.90 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.902, 90.902, 133.737, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 22.5

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) 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 (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) (pdb code 5wfm). 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 (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024), PDB code: 5wfm:
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 (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024)


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 (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:57.3 occ:1.00 O2 A:KU5205 2.1 58.2 0.5 OD2 A:ASP108 2.1 45.1 1.0 O1 A:KU5205 2.1 58.0 0.5 O1 A:KU5205 2.2 57.8 0.5 NE2 A:HIS41 2.2 49.6 1.0 O A:ILE120 2.2 56.9 1.0 O2 A:KU5205 2.2 58.8 0.5 OD1 A:ASP119 2.3 62.4 1.0 C4 A:KU5205 2.8 59.3 0.5 C3 A:KU5205 2.9 61.1 0.5 C4 A:KU5205 2.9 59.3 0.5 CE1 A:HIS41 2.9 54.9 1.0 C3 A:KU5205 3.0 61.0 0.5 CG A:ASP108 3.1 55.4 1.0 CD2 A:HIS41 3.3 51.1 1.0 C A:ILE120 3.3 57.3 1.0 OD1 A:ASP108 3.3 54.0 1.0 CG A:ASP119 3.5 63.6 1.0 N A:ILE120 3.6 53.9 1.0 MN A:MN202 3.7 64.2 1.0 CA A:ILE120 4.0 52.8 1.0 O A:HOH303 4.0 48.9 1.0 ND1 A:HIS41 4.1 47.0 1.0 OD2 A:ASP119 4.1 70.2 1.0 N1 A:KU5205 4.2 60.2 0.5 C A:ASP119 4.2 61.2 1.0 C2 A:KU5205 4.2 64.7 0.5 N1 A:KU5205 4.2 60.8 0.5 CG A:HIS41 4.3 54.3 1.0 C2 A:KU5205 4.3 65.0 0.5 O A:HOH310 4.3 61.0 1.0 N A:GLY121 4.4 63.7 1.0 CB A:ASP108 4.4 45.6 1.0 CA A:ASP119 4.5 57.0 1.0 CB A:ILE120 4.5 55.5 1.0 CB A:ASP119 4.6 60.9 1.0 O3 A:KU5205 4.7 67.8 0.5 CA A:GLY121 4.7 55.2 1.0 O3 A:KU5205 4.8 67.3 0.5 OE1 A:GLU80 4.8 59.9 1.0 C5 A:KU5205 4.9 67.8 0.5 C22 A:KU5205 5.0 72.3 0.5 O A:ASP119 5.0 64.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024)


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 (E119D Mutant) in Complex with Inhibitor 10E (Sri-30024) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:64.2 occ:1.00 O3 A:KU5205 1.9 67.8 0.5 O3 A:KU5205 2.0 67.3 0.5 OD1 A:ASP108 2.1 54.0 1.0 O A:HOH311 2.2 57.7 1.0 O2 A:KU5205 2.2 58.8 0.5 O2 A:KU5205 2.2 58.2 0.5 OE1 A:GLU80 2.3 59.9 1.0 O A:HOH303 2.4 48.9 1.0 C5 A:KU5205 2.9 67.8 0.5 C5 A:KU5205 3.1 68.1 0.5 CG A:ASP108 3.2 55.4 1.0 C3 A:KU5205 3.2 61.1 0.5 C3 A:KU5205 3.3 61.0 0.5 CD A:GLU80 3.4 61.8 1.0 C2 A:KU5205 3.5 64.7 0.5 C2 A:KU5205 3.6 65.0 0.5 OD2 A:ASP108 3.7 45.1 1.0 MN A:MN201 3.7 57.3 1.0 CE1 A:HIS41 3.8 54.9 1.0 O A:HOH324 4.0 53.9 1.0 N3 A:KU5205 4.1 69.8 0.5 O A:PRO107 4.1 58.9 1.0 OE2 A:GLU80 4.2 69.4 1.0 C23 A:KU5205 4.2 71.2 0.5 N3 A:KU5205 4.3 71.1 0.5 C22 A:KU5205 4.3 72.3 0.5 O A:LEU106 4.3 61.1 1.0 CG A:GLU80 4.4 46.6 1.0 CB A:ASP108 4.4 45.6 1.0 NE2 A:HIS41 4.4 49.6 1.0 C A:PRO107 4.4 60.5 1.0 C4 A:KU5205 4.5 59.3 0.5 CA A:ASP108 4.5 51.9 1.0 C4 A:KU5205 4.5 59.3 0.5 CB A:GLU80 4.5 46.8 1.0 C6 A:KU5205 4.5 71.9 0.5 N A:ASP108 4.6 57.0 1.0 C7 A:KU5205 4.6 75.6 0.5 C13 A:KU5205 4.6 73.1 0.5 OD1 A:ASP119 4.7 62.4 1.0 C6 A:KU5205 4.7 72.5 0.5 C9 A:KU5205 4.7 90.0 0.5 ND1 A:HIS41 4.8 47.0 1.0 C24 A:KU5205 4.8 90.2 0.5 O1 A:KU5205 4.8 57.8 0.5 C23 A:KU5205 4.8 89.8 0.5 N2 A:KU5205 4.9 66.0 0.5 O1 A:KU5205 4.9 58.0 0.5 N2 A:KU5205 5.0 66.2 0.5

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