Manganese in PDB 5wdc: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9E (Sri-29843)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9E (Sri-29843), PDB code: 5wdc 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)	38.87 / 2.10
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.777, 90.777, 134.545, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 24.2

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9E (Sri-29843) 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 9E (Sri-29843) (pdb code 5wdc). 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 9E (Sri-29843), PDB code: 5wdc:
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 9E (Sri-29843)


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 9E (Sri-29843) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:63.4 occ:1.00 OD2 A:ASP108 1.9 80.5 1.0 O1 A:G2K205 2.2 67.0 1.0 OE2 A:GLU119 2.2 68.3 1.0 O A:ILE120 2.3 59.9 1.0 O2 A:G2K205 2.4 65.5 1.0 NE2 A:HIS41 2.4 65.1 1.0 C1 A:G2K205 2.9 69.9 1.0 CG A:ASP108 3.0 77.6 1.0 CD A:GLU119 3.0 71.2 1.0 C2 A:G2K205 3.1 60.4 1.0 CE1 A:HIS41 3.1 62.2 1.0 C A:ILE120 3.4 75.2 1.0 OD1 A:ASP108 3.4 70.4 1.0 OE1 A:GLU119 3.4 65.2 1.0 CD2 A:HIS41 3.5 62.1 1.0 N A:ILE120 3.6 60.5 1.0 MN A:MN202 3.7 77.0 1.0 O A:HOH301 3.9 66.0 1.0 CA A:ILE120 3.9 61.0 1.0 CG A:GLU119 4.1 72.5 1.0 CB A:ASP108 4.2 59.0 1.0 N4 A:G2K205 4.2 63.4 1.0 CB A:ILE120 4.2 64.5 1.0 ND1 A:HIS41 4.3 65.1 1.0 C3 A:G2K205 4.4 67.0 1.0 C A:GLU119 4.4 67.0 1.0 O A:HOH309 4.5 61.2 1.0 CG A:HIS41 4.5 71.0 1.0 N A:GLY121 4.5 71.6 1.0 CA A:GLU119 4.7 63.0 1.0 CA A:GLY121 4.9 62.6 1.0 O3 A:G2K205 4.9 72.4 1.0 OE1 A:GLU80 5.0 87.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 9E (Sri-29843)


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 9E (Sri-29843) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:77.0 occ:1.00 OD1 A:ASP108 1.8 70.4 1.0 O2 A:G2K205 2.0 65.5 1.0 O3 A:G2K205 2.0 72.4 1.0 OE2 A:GLU80 2.3 99.3 1.0 O A:HOH301 2.4 66.0 1.0 O A:HOH303 2.5 60.1 1.0 CD A:GLU80 2.9 89.4 1.0 CG A:ASP108 2.9 77.6 1.0 C4 A:G2K205 3.0 75.0 1.0 C2 A:G2K205 3.0 60.4 1.0 OE1 A:GLU80 3.1 87.1 1.0 OD2 A:ASP108 3.3 80.5 1.0 C3 A:G2K205 3.5 67.0 1.0 MN A:MN201 3.7 63.4 1.0 CE1 A:HIS41 3.9 62.2 1.0 O A:HOH307 4.0 72.4 1.0 CG A:GLU80 4.1 66.9 1.0 CB A:ASP108 4.2 59.0 1.0 CB A:GLU80 4.2 56.4 1.0 N1 A:G2K205 4.2 80.0 1.0 C1 A:G2K205 4.2 69.9 1.0 OE1 A:GLU119 4.3 65.2 1.0 O A:PRO107 4.4 62.0 1.0 O A:LEU106 4.4 75.4 1.0 CA A:ASP108 4.4 69.5 1.0 NE2 A:HIS41 4.5 65.1 1.0 C A:PRO107 4.5 71.6 1.0 N A:ASP108 4.6 62.9 1.0 O1 A:G2K205 4.6 67.0 1.0 OE2 A:GLU119 4.6 68.3 1.0 C5 A:G2K205 4.7 84.4 1.0 N2 A:G2K205 4.8 66.5 1.0 ND1 A:HIS41 4.9 65.1 1.0 CD A:GLU119 4.9 71.2 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