Manganese in PDB 5wei: Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770), PDB code: 5wei 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)	38.33 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.474, 89.474, 133.662, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.1

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770) (pdb code 5wei). 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 (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770), PDB code: 5wei:
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 (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770)


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 (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:74.3 occ:1.00 O05 A:GY6206 2.2 96.2 1.0 OD1 A:ASP108 2.2 77.9 1.0 O A:ILE120 2.2 70.0 1.0 O08 A:GY6206 2.2 0.2 1.0 NE2 A:HIS41 2.3 66.3 1.0 OD1 A:ASP119 2.4 90.4 1.0 C07 A:GY6206 2.9 0.5 1.0 C04 A:GY6206 3.0 0.5 1.0 CG A:ASP108 3.1 78.8 1.0 CE1 A:HIS41 3.3 66.8 1.0 CD2 A:HIS41 3.3 58.1 1.0 OD2 A:ASP108 3.3 81.3 1.0 C A:ILE120 3.4 71.5 1.0 CG A:ASP119 3.6 89.8 1.0 N A:ILE120 3.6 57.6 1.0 MN A:MN202 3.7 0.5 1.0 O A:HOH302 3.7 81.5 1.0 CA A:ILE120 4.0 59.5 1.0 N09 A:GY6206 4.2 1.0 1.0 OD2 A:ASP119 4.3 97.1 1.0 C03 A:GY6206 4.3 0.2 1.0 C A:ASP119 4.3 63.1 1.0 ND1 A:HIS41 4.4 65.4 1.0 CG A:HIS41 4.4 65.7 1.0 N A:GLY121 4.4 69.9 1.0 CB A:ASP108 4.5 60.5 1.0 CA A:ASP119 4.5 68.8 1.0 CB A:ILE120 4.6 61.2 1.0 CA A:GLY121 4.7 63.5 1.0 O A:HOH309 4.7 80.5 1.0 CB A:ASP119 4.7 80.4 1.0 O12 A:GY6206 4.8 0.4 1.0 SG A:CYS45 5.0 63.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770)


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 (E119D Mutant) in Complex with Inhibitor 7A (Sri-29770) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:0.5 occ:1.00 OD2 A:ASP108 2.0 81.3 1.0 O12 A:GY6206 2.1 0.4 1.0 O05 A:GY6206 2.3 96.2 1.0 OE1 A:GLU80 2.4 91.8 1.0 O A:HOH304 2.7 93.7 1.0 O A:HOH302 2.8 81.5 1.0 C11 A:GY6206 3.1 0.4 1.0 CG A:ASP108 3.2 78.8 1.0 C04 A:GY6206 3.2 0.5 1.0 CD A:GLU80 3.3 86.4 1.0 CE1 A:HIS41 3.4 66.8 1.0 C03 A:GY6206 3.6 0.2 1.0 MN A:MN201 3.7 74.3 1.0 OD1 A:ASP108 3.7 77.9 1.0 NE2 A:HIS41 3.9 66.3 1.0 CG A:GLU80 4.1 68.9 1.0 OE2 A:GLU80 4.1 0.8 1.0 O A:PRO107 4.1 62.3 1.0 CB A:GLU80 4.2 57.9 1.0 N13 A:GY6206 4.3 0.8 1.0 CB A:ASP108 4.4 60.5 1.0 O A:LEU106 4.4 74.1 1.0 C07 A:GY6206 4.5 0.5 1.0 CA A:ASP108 4.5 59.7 1.0 ND1 A:HIS41 4.5 65.4 1.0 C A:PRO107 4.5 67.8 1.0 N A:ASP108 4.7 63.6 1.0 CA A:GLU80 4.8 62.2 1.0 C14 A:GY6206 4.8 1.0 1.0 O08 A:GY6206 4.8 0.2 1.0 N02 A:GY6206 4.9 0.4 1.0 OD1 A:ASP119 4.9 90.4 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