Manganese in PDB 5wb3: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10J (Sri-30026)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10J (Sri-30026), PDB code: 5wb3 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)	37.58 / 2.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.698, 90.698, 134.310, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 24.2

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10J (Sri-30026) 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 10J (Sri-30026) (pdb code 5wb3). 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 10J (Sri-30026), PDB code: 5wb3:
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 10J (Sri-30026)


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 10J (Sri-30026) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:62.9 occ:1.00 O1 A:GYA205 2.0 67.2 1.0 OD2 A:ASP108 2.1 62.7 1.0 NE2 A:HIS41 2.2 59.5 1.0 O2 A:GYA205 2.2 58.3 1.0 O A:ILE120 2.3 58.9 1.0 OE1 A:GLU119 2.3 62.4 1.0 C1 A:GYA205 2.7 63.1 1.0 C2 A:GYA205 2.9 57.7 1.0 CE1 A:HIS41 2.9 58.0 1.0 CG A:ASP108 2.9 62.8 1.0 CD A:GLU119 3.2 64.2 1.0 OD1 A:ASP108 3.2 60.1 1.0 CD2 A:HIS41 3.3 58.0 1.0 C A:ILE120 3.4 61.6 1.0 OE2 A:GLU119 3.6 62.1 1.0 MN A:MN202 3.7 67.9 1.0 N A:ILE120 3.7 61.7 1.0 O A:HOH301 3.8 55.0 1.0 N4 A:GYA205 4.0 63.3 1.0 CA A:ILE120 4.1 62.9 1.0 ND1 A:HIS41 4.1 54.5 1.0 C3 A:GYA205 4.2 65.0 1.0 CG A:GLU119 4.3 68.2 1.0 CG A:HIS41 4.3 62.2 1.0 O A:HOH308 4.3 64.5 1.0 CB A:ASP108 4.4 61.0 1.0 CB A:ILE120 4.5 67.5 1.0 N A:GLY121 4.5 63.9 1.0 C A:GLU119 4.6 65.8 1.0 CA A:GLY121 4.8 58.6 1.0 O5 A:GYA205 4.8 68.6 1.0 CA A:GLU119 5.0 65.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10J (Sri-30026)


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 10J (Sri-30026) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:67.9 occ:1.00 O5 A:GYA205 2.0 68.6 1.0 O2 A:GYA205 2.0 58.3 1.0 OD1 A:ASP108 2.1 60.1 1.0 O A:HOH305 2.3 65.8 1.0 O A:HOH301 2.3 55.0 1.0 OE1 A:GLU80 2.5 58.9 1.0 C4 A:GYA205 3.0 68.3 1.0 C2 A:GYA205 3.1 57.7 1.0 CG A:ASP108 3.2 62.8 1.0 C3 A:GYA205 3.5 65.0 1.0 CD A:GLU80 3.6 66.6 1.0 OD2 A:ASP108 3.7 62.7 1.0 MN A:MN201 3.7 62.9 1.0 CE1 A:HIS41 3.9 58.0 1.0 CB A:GLU80 4.1 61.1 1.0 N1 A:GYA205 4.2 77.4 1.0 O A:PRO107 4.3 59.9 1.0 C1 A:GYA205 4.3 63.1 1.0 CG A:GLU80 4.3 63.0 1.0 OE2 A:GLU119 4.3 62.1 1.0 CB A:ASP108 4.3 61.0 1.0 O A:LEU106 4.4 68.9 1.0 CA A:ASP108 4.4 61.8 1.0 NE2 A:HIS41 4.5 59.5 1.0 C A:PRO107 4.5 64.7 1.0 OE1 A:GLU119 4.5 62.4 1.0 N A:ASP108 4.6 61.9 1.0 OE2 A:GLU80 4.6 69.4 1.0 C5 A:GYA205 4.6 82.6 1.0 O1 A:GYA205 4.7 67.2 1.0 ND1 A:HIS41 4.8 54.5 1.0 N2 A:GYA205 4.8 69.2 1.0 CD A:GLU119 4.9 64.2 1.0 CA A:GLU80 4.9 57.3 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