Manganese in PDB 5wg9: Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9B (Sri-30101)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 9B (Sri-30101), PDB code: 5wg9 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)	32.04 / 2.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.612, 90.612, 133.788, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.1

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) 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 (E119D Mutant) in Complex with Inhibitor 9B (Sri-30101) (pdb code 5wg9). 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 9B (Sri-30101), PDB code: 5wg9:
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 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 (E119D Mutant) in Complex with Inhibitor 9B (Sri-30101) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:67.2 occ:1.00 O2 A:KU4205 2.0 76.7 1.0 OD2 A:ASP108 2.1 58.7 1.0 NE2 A:HIS41 2.2 62.8 1.0 O1 A:KU4205 2.2 78.2 1.0 O A:ILE120 2.2 62.1 1.0 OD1 A:ASP119 2.3 79.2 1.0 C1 A:KU4205 2.8 81.8 1.0 C2 A:KU4205 2.9 80.7 1.0 CE1 A:HIS41 2.9 61.4 1.0 CG A:ASP108 3.0 63.1 1.0 OD1 A:ASP108 3.2 65.0 1.0 C A:ILE120 3.3 60.1 1.0 CD2 A:HIS41 3.3 62.5 1.0 N A:ILE120 3.4 54.8 1.0 CG A:ASP119 3.4 80.0 1.0 MN A:MN202 3.7 77.6 1.0 O A:HOH301 3.8 57.8 1.0 CA A:ILE120 3.9 57.1 1.0 OD2 A:ASP119 4.0 84.9 1.0 ND1 A:HIS41 4.1 62.0 1.0 NZ A:LYS134 4.1 86.6 1.0 C3 A:KU4205 4.2 81.8 1.0 N4 A:KU4205 4.2 86.4 1.0 C A:ASP119 4.2 62.2 1.0 CG A:HIS41 4.3 62.3 1.0 N A:GLY121 4.4 65.9 1.0 CB A:ASP108 4.4 55.5 1.0 CB A:ILE120 4.4 64.8 1.0 CA A:ASP119 4.5 64.4 1.0 CB A:ASP119 4.6 73.8 1.0 O4 A:KU4205 4.6 84.4 1.0 CA A:GLY121 4.8 63.3 1.0 O A:HOH312 4.8 76.3 1.0 CE A:LYS134 4.9 90.2 1.0 C4 A:KU4205 4.9 85.2 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 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 (E119D Mutant) in Complex with Inhibitor 9B (Sri-30101) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:77.6 occ:1.00 O4 A:KU4205 1.9 84.4 1.0 OD1 A:ASP108 2.1 65.0 1.0 O A:HOH304 2.3 64.6 1.0 O2 A:KU4205 2.3 76.7 1.0 O A:HOH301 2.3 57.8 1.0 OE1 A:GLU80 2.4 61.7 1.0 C4 A:KU4205 3.0 85.2 1.0 CG A:ASP108 3.2 63.1 1.0 C2 A:KU4205 3.3 80.7 1.0 CD A:GLU80 3.6 63.9 1.0 C3 A:KU4205 3.6 81.8 1.0 MN A:MN201 3.7 67.2 1.0 CE1 A:HIS41 3.8 61.4 1.0 OD2 A:ASP108 3.8 58.7 1.0 O A:LEU106 4.1 70.1 1.0 N1 A:KU4205 4.2 89.0 1.0 O A:PRO107 4.2 64.9 1.0 CG A:GLU80 4.3 55.4 1.0 CB A:ASP108 4.4 55.5 1.0 NE2 A:HIS41 4.4 62.8 1.0 CB A:GLU80 4.4 54.0 1.0 C A:PRO107 4.4 62.2 1.0 CA A:ASP108 4.5 55.6 1.0 OE2 A:GLU80 4.5 77.2 1.0 C21 A:KU4205 4.5 91.0 1.0 N A:ASP108 4.5 57.3 1.0 C1 A:KU4205 4.6 81.8 1.0 C5 A:KU4205 4.6 91.5 1.0 OD1 A:ASP119 4.7 79.2 1.0 ND1 A:HIS41 4.7 62.0 1.0 C22 A:KU4205 4.9 94.7 1.0 N2 A:KU4205 4.9 83.4 1.0 O1 A:KU4205 5.0 78.2 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