Manganese in PDB 5des: 2009 H1N1 Pa Endonuclease Domain

The structure of 2009 H1N1 Pa Endonuclease Domain, PDB code: 5des 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)	43.00 / 2.05
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.619, 73.619, 129.056, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 23.3

The binding sites of Manganese atom in the 2009 H1N1 Pa Endonuclease Domain (pdb code 5des). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 2009 H1N1 Pa Endonuclease Domain, PDB code: 5des:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2009 H1N1 Pa Endonuclease Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2009 H1N1 Pa Endonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:49.1 occ:1.00 OD2 A:ASP108 2.1 27.2 1.0 O A:HOH464 2.2 35.4 1.0 O A:ILE120 2.3 32.8 1.0 OE1 A:GLU119 2.4 39.0 1.0 O A:HOH421 2.4 50.0 1.0 NE2 A:HIS41 2.5 28.0 1.0 CG A:ASP108 3.0 28.1 1.0 OD1 A:ASP108 3.1 26.0 1.0 CE1 A:HIS41 3.2 27.0 1.0 CD A:GLU119 3.3 39.4 1.0 C A:ILE120 3.4 33.4 1.0 CD2 A:HIS41 3.5 27.8 1.0 MN A:MN302 3.6 55.6 1.0 N A:ILE120 3.7 33.2 1.0 OE2 A:GLU119 3.7 37.8 1.0 CA A:ILE120 4.0 34.5 1.0 O A:HOH407 4.0 30.0 1.0 NZ A:LYS134 4.1 49.8 1.0 ND1 A:HIS41 4.3 26.6 1.0 CB A:ASP108 4.4 28.4 1.0 CB A:ILE120 4.4 35.2 1.0 CG A:GLU119 4.5 37.1 1.0 CG A:HIS41 4.5 27.3 1.0 N A:GLY121 4.5 33.4 1.0 OE1 A:GLU80 4.6 29.2 1.0 C A:GLU119 4.7 33.7 1.0 CE A:LYS134 4.8 50.4 1.0 CA A:GLY121 4.8 32.7 1.0 SG A:CYS45 4.8 28.6 1.0 CA A:GLU119 5.0 33.7 1.0

Manganese binding site 2 out of 2 in the 2009 H1N1 Pa Endonuclease Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2009 H1N1 Pa Endonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:55.6 occ:1.00 OD1 A:ASP108 2.1 26.0 1.0 O A:HOH407 2.1 30.0 1.0 O A:HOH459 2.1 32.1 1.0 O A:HOH464 2.1 35.4 1.0 OE1 A:GLU80 2.2 29.2 1.0 O A:HOH427 2.3 28.8 1.0 CG A:ASP108 3.2 28.1 1.0 CD A:GLU80 3.2 29.8 1.0 MN A:MN301 3.6 49.1 1.0 OD2 A:ASP108 3.8 27.2 1.0 OE2 A:GLU80 4.0 32.3 1.0 CE1 A:HIS41 4.1 27.0 1.0 CG A:GLU80 4.1 29.3 1.0 O A:HOH429 4.2 48.2 1.0 O A:HOH444 4.2 41.3 1.0 CB A:GLU80 4.2 28.4 1.0 O A:PRO107 4.2 27.4 1.0 OE2 A:GLU119 4.3 37.8 1.0 O A:HOH476 4.3 40.4 1.0 O A:LEU106 4.3 29.4 1.0 C A:PRO107 4.4 28.3 1.0 CB A:ASP108 4.4 28.4 1.0 CA A:ASP108 4.4 27.7 1.0 N A:ASP108 4.5 27.4 1.0 OE1 A:GLU119 4.6 39.0 1.0 NE2 A:HIS41 4.6 28.0 1.0 CA A:GLU80 4.8 28.1 1.0 CD A:GLU119 4.8 39.4 1.0 O A:HOH421 4.9 50.0 1.0

M.S.Song, G.Kumar, W.R.Shadrick, W.Zhou, T.Jeevan, Z.Li, P.J.Slavish, T.P.Fabrizio, S.W.Yoon, T.R.Webb, R.J.Webby, S.W.White. Identification and Characterization of Influenza Variants Resistant to A Viral Endonuclease Inhibitor. Proc.Natl.Acad.Sci.Usa V. 113 3669 2016.
ISSN: ESSN 1091-6490
PubMed: 26976575
DOI: 10.1073/PNAS.1519772113