Manganese in PDB 5w3i: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6E (Sri-29685)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6E (Sri-29685), PDB code: 5w3i 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)	35.33 / 1.95
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.162, 61.162, 94.813, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.1

The binding sites of Manganese atom in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6E (Sri-29685) (pdb code 5w3i). 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 6E (Sri-29685), PDB code: 5w3i:
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 6E (Sri-29685)


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 6E (Sri-29685) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:10.2 occ:1.00 H02 A:GY5304 1.8 15.7 1.0 O02 A:GY5304 2.1 12.0 1.0 O01 A:GY5304 2.2 13.1 1.0 OD1 A:ASP108 2.2 9.8 1.0 O A:ILE120 2.2 9.7 1.0 OE1 A:GLU119 2.3 12.4 1.0 NE2 A:HIS41 2.3 9.7 1.0 C04 A:GY5304 2.8 13.1 1.0 C03 A:GY5304 2.9 12.6 1.0 CG A:ASP108 3.0 9.8 1.0 CE1 A:HIS41 3.1 9.8 1.0 HE1 A:HIS41 3.2 11.7 1.0 OD2 A:ASP108 3.2 9.9 1.0 H A:ILE120 3.3 11.6 1.0 CD A:GLU119 3.3 14.7 1.0 C A:ILE120 3.3 9.6 1.0 CD2 A:HIS41 3.4 9.7 1.0 HD2 A:HIS41 3.6 11.6 1.0 HB A:ILE120 3.6 12.2 1.0 MN A:MN302 3.7 13.2 1.0 HZ1 A:LYS134 3.7 57.5 1.0 OE2 A:GLU119 3.8 15.9 1.0 N A:ILE120 3.8 9.7 1.0 O A:HOH411 3.9 11.4 1.0 CA A:ILE120 4.0 9.5 1.0 HA2 A:GLY121 4.1 12.5 1.0 N02 A:GY5304 4.2 19.8 1.0 ND1 A:HIS41 4.2 9.8 1.0 C02 A:GY5304 4.2 19.5 1.0 HG3 A:GLU119 4.2 15.8 1.0 CB A:ILE120 4.3 10.2 1.0 H A:GY5304 4.3 63.2 1.0 O A:HOH430 4.3 14.5 1.0 CG A:HIS41 4.4 10.2 1.0 CG A:GLU119 4.4 13.2 1.0 N A:GLY121 4.4 10.3 1.0 CB A:ASP108 4.4 9.8 1.0 H01 A:GY5304 4.5 23.8 1.0 NZ A:LYS134 4.5 48.0 1.0 HE3 A:LYS134 4.5 59.1 1.0 HZ2 A:LYS134 4.6 57.5 1.0 HB2 A:ASP108 4.6 11.6 1.0 HA A:GLU119 4.6 14.4 1.0 HG22 A:ILE120 4.7 11.1 1.0 CA A:GLY121 4.7 10.4 1.0 OE2 A:GLU80 4.7 11.1 1.0 C A:GLU119 4.8 11.6 1.0 HB3 A:ASP108 4.8 11.6 1.0 HA A:ILE120 4.9 11.4 1.0 HD1 A:HIS41 4.9 11.8 1.0 O03 A:GY5304 5.0 12.5 1.0 CE A:LYS134 5.0 49.2 1.0 C A:GY5304 5.0 52.7 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 6E (Sri-29685)


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 6E (Sri-29685) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:13.2 occ:1.00 O03 A:GY5304 2.0 12.5 1.0 O01 A:GY5304 2.1 13.1 1.0 OD2 A:ASP108 2.1 9.9 1.0 OE2 A:GLU80 2.1 11.1 1.0 O A:HOH411 2.2 11.4 1.0 H02 A:GY5304 2.3 15.7 1.0 O A:HOH428 2.3 10.8 1.0 C05 A:GY5304 3.0 21.0 1.0 C03 A:GY5304 3.1 12.6 1.0 HE1 A:HIS41 3.1 11.7 1.0 CG A:ASP108 3.2 9.8 1.0 CD A:GLU80 3.2 14.0 1.0 C02 A:GY5304 3.4 19.5 1.0 MN A:MN301 3.7 10.2 1.0 OD1 A:ASP108 3.7 9.8 1.0 HB2 A:GLU80 3.8 12.8 1.0 CE1 A:HIS41 3.8 9.8 1.0 HA A:ASP108 3.9 12.0 1.0 H120 A:GY5304 3.9 69.9 1.0 HG2 A:GLU80 4.0 15.3 1.0 OE1 A:GLU80 4.1 11.6 1.0 CG A:GLU80 4.1 12.8 1.0 O A:HOH461 4.1 15.7 1.0 O A:HOH452 4.2 25.7 1.0 O A:PRO107 4.2 10.9 1.0 N03 A:GY5304 4.3 31.1 1.0 CB A:ASP108 4.4 9.8 1.0 CB A:GLU80 4.4 10.7 1.0 OE2 A:GLU119 4.4 15.9 1.0 NE2 A:HIS41 4.4 9.7 1.0 O A:LEU106 4.4 15.6 1.0 C04 A:GY5304 4.4 13.1 1.0 CA A:ASP108 4.4 10.1 1.0 HA A:GLU80 4.4 13.2 1.0 C A:PRO107 4.5 10.8 1.0 OE1 A:GLU119 4.5 12.4 1.0 H03 A:GY5304 4.5 46.0 1.0 C13 A:GY5304 4.5 58.2 1.0 N A:ASP108 4.6 10.4 1.0 H A:GY5304 4.6 63.2 1.0 HB3 A:ASP108 4.8 11.6 1.0 ND1 A:HIS41 4.8 9.8 1.0 N01 A:GY5304 4.8 22.0 1.0 O02 A:GY5304 4.8 12.0 1.0 C A:GY5304 4.9 52.7 1.0 CD A:GLU119 4.9 14.7 1.0 C06 A:GY5304 4.9 38.3 1.0 H04 A:GY5304 5.0 37.3 1.0 CA A:GLU80 5.0 11.0 1.0 HG3 A:GLU80 5.0 15.3 1.0 HD1 A:HIS41 5.0 11.8 1.0 HA A:PRO107 5.0 15.4 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