Manganese in PDB 5w9g: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9K (Sri-30023)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9K (Sri-30023), PDB code: 5w9g was solved by G.Kumar, S.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.68 / 2.10
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.249, 90.249, 135.307, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 24.1

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9K (Sri-30023) 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 in Complex with Inhibitor 9K (Sri-30023) (pdb code 5w9g). 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 9K (Sri-30023), PDB code: 5w9g:
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 9K (Sri-30023)


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 9K (Sri-30023) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:69.3 occ:1.00 OE2 A:GLU119 2.1 76.9 1.0 O2 A:KU2204 2.1 75.1 1.0 NE2 A:HIS41 2.2 68.4 1.0 OD2 A:ASP108 2.2 63.5 1.0 O A:ILE120 2.3 64.4 1.0 O1 A:KU2204 2.4 63.2 1.0 CE1 A:HIS41 2.9 63.3 1.0 C4 A:KU2204 2.9 68.4 1.0 CG A:ASP108 2.9 75.8 1.0 OD1 A:ASP108 3.0 61.5 1.0 C3 A:KU2204 3.0 65.2 1.0 CD A:GLU119 3.1 72.0 1.0 CD2 A:HIS41 3.3 63.8 1.0 C A:ILE120 3.4 78.1 1.0 OE1 A:GLU119 3.4 72.9 1.0 MN A:MN202 3.7 81.3 1.0 N A:ILE120 3.8 64.6 1.0 O A:HOH302 3.8 61.6 1.0 ND1 A:HIS41 4.0 63.4 1.0 CA A:ILE120 4.1 76.2 1.0 N2 A:KU2204 4.2 73.2 1.0 CG A:HIS41 4.3 76.8 1.0 C2 A:KU2204 4.3 69.6 1.0 CB A:ASP108 4.4 58.9 1.0 CG A:GLU119 4.4 71.4 1.0 CB A:ILE120 4.5 81.8 1.0 O A:HOH306 4.5 63.9 1.0 N A:GLY121 4.5 73.1 1.0 C A:GLU119 4.6 81.2 1.0 CA A:GLY121 4.8 70.5 1.0 O3 A:KU2204 4.9 73.9 1.0 CA A:GLU119 5.0 69.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9K (Sri-30023)


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 9K (Sri-30023) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:81.3 occ:1.00 O1 A:KU2204 2.0 63.2 1.0 O3 A:KU2204 2.1 73.9 1.0 OD1 A:ASP108 2.2 61.5 1.0 OE1 A:GLU80 2.2 68.1 1.0 O A:HOH303 2.2 71.0 1.0 O A:HOH302 2.3 61.6 1.0 C5 A:KU2204 3.1 76.7 1.0 C3 A:KU2204 3.2 65.2 1.0 CG A:ASP108 3.3 75.8 1.0 CD A:GLU80 3.4 89.1 1.0 C2 A:KU2204 3.6 69.6 1.0 MN A:MN201 3.7 69.3 1.0 CE1 A:HIS41 3.8 63.3 1.0 OD2 A:ASP108 4.0 63.5 1.0 CB A:GLU80 4.1 71.0 1.0 CG A:GLU80 4.1 71.7 1.0 O A:PRO107 4.3 71.1 1.0 O A:LEU106 4.3 78.0 1.0 OE2 A:GLU80 4.3 76.3 1.0 N3 A:KU2204 4.3 82.5 1.0 CB A:ASP108 4.4 58.9 1.0 OE1 A:GLU119 4.4 72.9 1.0 C4 A:KU2204 4.4 68.4 1.0 NE2 A:HIS41 4.4 68.4 1.0 CA A:ASP108 4.5 67.6 1.0 C A:PRO107 4.5 79.5 1.0 N A:ASP108 4.6 67.8 1.0 ND1 A:HIS41 4.7 63.4 1.0 O2 A:KU2204 4.7 75.1 1.0 C12 A:KU2204 4.9 93.6 1.0 CA A:GLU80 4.9 65.7 1.0 OE2 A:GLU119 4.9 76.9 1.0 N1 A:KU2204 4.9 81.7 1.0 CL1 A:KU2204 5.0 0.4 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