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

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 10E (Sri-30024), PDB code: 5web 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)	38.89 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.793, 90.793, 135.062, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.5

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease 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 in Complex with Inhibitor 10E (Sri-30024) (pdb code 5web). 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 10E (Sri-30024), PDB code: 5web:
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 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 in Complex with Inhibitor 10E (Sri-30024) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:78.4 occ:1.00 O1 A:KU5203 2.1 80.2 0.5 NE2 A:HIS41 2.1 73.3 1.0 OE2 A:GLU119 2.2 84.6 1.0 O1 A:KU5203 2.2 81.2 0.5 OD2 A:ASP108 2.3 82.2 1.0 O2 A:KU5203 2.3 79.7 0.5 O A:ILE120 2.3 71.5 1.0 O2 A:KU5203 2.4 79.9 0.5 CE1 A:HIS41 2.8 70.1 1.0 C4 A:KU5203 2.9 84.0 0.5 C4 A:KU5203 3.0 84.2 0.5 C3 A:KU5203 3.0 82.5 0.5 CG A:ASP108 3.0 80.7 1.0 CD A:GLU119 3.1 81.7 1.0 C3 A:KU5203 3.1 82.6 0.5 OD1 A:ASP108 3.1 83.1 1.0 CD2 A:HIS41 3.3 74.3 1.0 C A:ILE120 3.5 82.4 1.0 OE1 A:GLU119 3.5 83.9 1.0 MN A:MN202 3.7 84.6 1.0 N A:ILE120 3.8 76.5 1.0 O A:HOH302 4.0 71.5 1.0 ND1 A:HIS41 4.0 69.4 1.0 CA A:ILE120 4.1 75.6 1.0 O A:HOH306 4.2 83.6 1.0 N1 A:KU5203 4.2 87.2 0.5 CG A:GLU119 4.2 81.8 1.0 CG A:HIS41 4.2 79.2 1.0 N1 A:KU5203 4.3 88.0 0.5 C2 A:KU5203 4.3 86.0 0.5 CB A:ILE120 4.3 72.7 1.0 C2 A:KU5203 4.4 86.0 0.5 CB A:ASP108 4.5 73.0 1.0 N A:GLY121 4.6 85.8 1.0 C A:GLU119 4.6 83.2 1.0 O3 A:KU5203 4.9 82.3 0.5 CA A:GLY121 4.9 82.5 1.0 OE1 A:GLU80 4.9 75.4 1.0 O3 A:KU5203 4.9 83.6 0.5 CA A:GLU119 4.9 76.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease 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 in Complex with Inhibitor 10E (Sri-30024) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:84.6 occ:1.00 OD1 A:ASP108 2.0 83.1 1.0 O A:HOH302 2.0 71.5 1.0 O2 A:KU5203 2.2 79.9 0.5 O3 A:KU5203 2.2 83.6 0.5 O2 A:KU5203 2.2 79.7 0.5 O3 A:KU5203 2.2 82.3 0.5 O A:HOH303 2.3 81.7 1.0 OE1 A:GLU80 2.3 75.4 1.0 CG A:ASP108 3.1 80.7 1.0 C5 A:KU5203 3.2 88.0 0.5 C5 A:KU5203 3.3 88.3 0.5 C3 A:KU5203 3.3 82.6 0.5 C3 A:KU5203 3.3 82.5 0.5 CD A:GLU80 3.4 81.6 1.0 OD2 A:ASP108 3.7 82.2 1.0 MN A:MN201 3.7 78.4 1.0 C2 A:KU5203 3.7 86.0 0.5 C2 A:KU5203 3.8 86.0 0.5 O A:HOH312 3.9 92.5 1.0 CE1 A:HIS41 3.9 70.1 1.0 CG A:GLU80 4.2 75.6 1.0 OE1 A:GLU119 4.2 83.9 1.0 CB A:ASP108 4.2 73.0 1.0 CB A:GLU80 4.2 71.4 1.0 O A:PRO107 4.3 75.3 1.0 O A:LEU106 4.3 78.3 1.0 CA A:ASP108 4.3 76.5 1.0 OE2 A:GLU80 4.4 84.1 1.0 N3 A:KU5203 4.4 95.8 0.5 C A:PRO107 4.4 82.6 1.0 N A:ASP108 4.4 79.2 1.0 N3 A:KU5203 4.4 96.1 0.5 C4 A:KU5203 4.5 84.2 0.5 OE2 A:GLU119 4.5 84.6 1.0 C4 A:KU5203 4.5 84.0 0.5 NE2 A:HIS41 4.5 73.3 1.0 C24 A:KU5203 4.6 74.5 0.5 C9 A:KU5203 4.6 1.0 0.5 C9 A:KU5203 4.7 0.3 0.5 C7 A:KU5203 4.7 0.6 0.5 C7 A:KU5203 4.7 0.3 0.5 O1 A:KU5203 4.8 81.2 0.5 CD A:GLU119 4.8 81.7 1.0 ND1 A:HIS41 4.8 69.4 1.0 O1 A:KU5203 4.8 80.2 0.5 C6 A:KU5203 4.8 98.5 0.5 C10 A:KU5203 4.9 0.2 0.5 C6 A:KU5203 4.9 98.8 0.5 C10 A:KU5203 4.9 0.2 0.5 CA A:GLU80 5.0 67.8 1.0 C23 A:KU5203 5.0 79.5 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