Manganese in PDB 5dbs: 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with Dtmp

The structure of 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with Dtmp, PDB code: 5dbs 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)	50.00 / 2.11
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.390, 90.390, 133.293, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.1

The binding sites of Manganese atom in the 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with Dtmp (pdb code 5dbs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with Dtmp, PDB code: 5dbs:

Manganese binding site 1 out of 1 in the 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with Dtmp


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 Mutant E119D in Complex with Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:50.7 occ:1.00 O A:ILE120 2.0 49.8 1.0 O3P A:TMP303 2.1 64.3 1.0 OD2 A:ASP108 2.1 46.6 1.0 OD1 A:ASP119 2.3 64.6 1.0 NE2 A:HIS41 2.4 52.5 1.0 CE1 A:HIS41 3.0 50.9 1.0 CG A:ASP108 3.1 47.2 1.0 C A:ILE120 3.1 50.9 1.0 OD1 A:ASP108 3.4 46.2 1.0 CG A:ASP119 3.5 61.8 1.0 P A:TMP303 3.5 71.0 1.0 N A:ILE120 3.6 52.5 1.0 CD2 A:HIS41 3.6 51.1 1.0 CA A:ILE120 3.9 52.9 1.0 O5' A:TMP303 4.0 65.9 1.0 C5' A:TMP303 4.1 66.8 1.0 OD2 A:ASP119 4.1 66.4 1.0 NZ A:LYS134 4.2 71.8 1.0 N A:GLY121 4.2 50.5 1.0 C A:ASP119 4.2 54.2 1.0 O1P A:TMP303 4.2 54.9 1.0 ND1 A:HIS41 4.2 51.0 1.0 CA A:ASP119 4.5 54.6 1.0 CB A:ASP108 4.5 46.8 1.0 CA A:GLY121 4.5 48.6 1.0 CG A:HIS41 4.6 51.5 1.0 CB A:ASP119 4.6 58.5 1.0 CB A:ILE120 4.6 54.9 1.0 CE A:LYS134 4.6 72.3 1.0 O2P A:TMP303 4.6 72.5 1.0 O A:ASP119 4.9 55.1 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. V. 113 3669 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 26976575
DOI: 10.1073/PNAS.1519772113