Manganese in PDB 5wdw: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10K (Sri-30027)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10K (Sri-30027), PDB code: 5wdw 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)	32.08 / 2.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.744, 90.744, 135.876, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 28.5

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10K (Sri-30027) 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 10K (Sri-30027) (pdb code 5wdw). 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 10K (Sri-30027), PDB code: 5wdw:
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 10K (Sri-30027)


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 10K (Sri-30027) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:75.3 occ:1.00 OE1 A:GLU119 2.0 93.0 1.0 O1 A:8KU203 2.1 78.9 1.0 OD2 A:ASP108 2.1 77.2 1.0 NE2 A:HIS41 2.3 62.6 1.0 O A:ILE120 2.3 83.1 1.0 O2 A:8KU203 2.3 88.0 1.0 C1 A:8KU203 2.8 83.6 1.0 CE1 A:HIS41 2.9 65.1 1.0 C2 A:8KU203 3.0 88.1 1.0 CG A:ASP108 3.1 80.0 1.0 CD A:GLU119 3.1 83.8 1.0 OD1 A:ASP108 3.3 78.6 1.0 CD2 A:HIS41 3.4 63.7 1.0 C A:ILE120 3.4 80.0 1.0 OE2 A:GLU119 3.5 76.0 1.0 N A:ILE120 3.7 63.0 1.0 MN A:MN202 3.7 80.1 1.0 O A:HOH301 4.0 54.1 1.0 CA A:ILE120 4.0 69.4 1.0 ND1 A:HIS41 4.1 59.1 1.0 N4 A:8KU203 4.1 77.4 1.0 CG A:HIS41 4.3 66.9 1.0 C3 A:8KU203 4.3 87.7 1.0 CG A:GLU119 4.4 77.3 1.0 CB A:ILE120 4.4 73.4 1.0 CB A:ASP108 4.5 78.0 1.0 N A:GLY121 4.5 87.3 1.0 C A:GLU119 4.7 74.0 1.0 CA A:GLY121 4.8 78.3 1.0 O4 A:8KU203 4.9 79.3 1.0 OE2 A:GLU80 4.9 78.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10K (Sri-30027)


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 10K (Sri-30027) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:80.1 occ:1.00 O A:HOH302 1.9 77.1 1.0 OD1 A:ASP108 1.9 78.6 1.0 OE2 A:GLU80 2.0 78.2 1.0 O2 A:8KU203 2.1 88.0 1.0 O4 A:8KU203 2.1 79.3 1.0 O A:HOH301 2.3 54.1 1.0 CG A:ASP108 3.1 80.0 1.0 C4 A:8KU203 3.1 87.7 1.0 C2 A:8KU203 3.2 88.1 1.0 CD A:GLU80 3.2 75.4 1.0 C3 A:8KU203 3.6 87.7 1.0 OD2 A:ASP108 3.7 77.2 1.0 MN A:MN201 3.7 75.3 1.0 O A:PRO107 3.9 71.6 1.0 CG A:GLU80 4.1 68.7 1.0 OE1 A:GLU80 4.1 76.9 1.0 CE1 A:HIS41 4.1 65.1 1.0 O A:LEU106 4.2 66.3 1.0 C A:PRO107 4.3 75.8 1.0 CB A:ASP108 4.3 78.0 1.0 OE2 A:GLU119 4.3 76.0 1.0 N1 A:8KU203 4.3 90.5 1.0 CB A:GLU80 4.3 65.0 1.0 C1 A:8KU203 4.4 83.6 1.0 CA A:ASP108 4.4 74.6 1.0 N A:ASP108 4.5 75.2 1.0 O1 A:8KU203 4.7 78.9 1.0 NE2 A:HIS41 4.8 62.6 1.0 C5 A:8KU203 4.8 89.9 1.0 OE1 A:GLU119 4.8 93.0 1.0 N2 A:8KU203 5.0 91.3 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