Manganese in PDB 5ccy: 2009 H1N1 Pa Endonuclease in Complex with Dtmp

The structure of 2009 H1N1 Pa Endonuclease in Complex with Dtmp, PDB code: 5ccy 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)	50.01 / 2.10
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.908, 73.908, 128.282, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 24.4

The binding sites of Manganese atom in the 2009 H1N1 Pa Endonuclease in Complex with Dtmp (pdb code 5ccy). 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 in Complex with Dtmp, PDB code: 5ccy:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2009 H1N1 Pa Endonuclease 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 in Complex with Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:24.4 occ:1.00 O A:ILE120 2.1 25.1 1.0 OD2 A:ASP108 2.1 18.4 1.0 O2P A:TMP303 2.2 25.9 1.0 OE2 A:GLU119 2.2 26.9 1.0 O1P A:TMP303 2.2 26.8 1.0 NE2 A:HIS41 2.3 21.4 1.0 P A:TMP303 2.8 30.1 1.0 CG A:ASP108 3.0 21.6 1.0 CE1 A:HIS41 3.1 22.0 1.0 C A:ILE120 3.3 26.1 1.0 CD A:GLU119 3.3 27.1 1.0 OD1 A:ASP108 3.3 19.9 1.0 CD2 A:HIS41 3.3 23.0 1.0 MN A:MN302 3.7 41.3 1.0 N A:ILE120 3.7 25.4 1.0 OE1 A:GLU119 3.8 25.1 1.0 CA A:ILE120 3.9 27.1 1.0 O3P A:TMP303 3.9 28.6 1.0 O A:HOH404 4.0 23.6 1.0 O5' A:TMP303 4.0 29.6 1.0 NZ A:LYS134 4.0 31.3 1.0 ND1 A:HIS41 4.2 21.7 1.0 C5' A:TMP303 4.2 33.8 1.0 CB A:ILE120 4.3 29.2 1.0 O A:HOH431 4.3 28.3 1.0 N A:GLY121 4.3 27.2 1.0 CG A:HIS41 4.4 22.0 1.0 CB A:ASP108 4.5 21.2 1.0 CG A:GLU119 4.5 27.5 1.0 CE A:LYS134 4.5 34.0 1.0 OE2 A:GLU80 4.7 23.2 1.0 CA A:GLY121 4.7 25.3 1.0 C A:GLU119 4.7 26.5 1.0 CG2 A:ILE120 4.9 28.8 1.0

Manganese binding site 2 out of 2 in the 2009 H1N1 Pa Endonuclease in Complex with Dtmp


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 in Complex with Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:41.3 occ:1.00 O2P A:TMP303 2.1 25.9 1.0 OE2 A:GLU80 2.1 23.2 1.0 OD1 A:ASP108 2.2 19.9 1.0 O A:HOH404 2.2 23.6 1.0 O A:HOH473 2.2 20.9 1.0 O A:HOH445 2.3 24.4 1.0 CD A:GLU80 3.2 25.1 1.0 CG A:ASP108 3.2 21.6 1.0 P A:TMP303 3.4 30.1 1.0 MN A:MN301 3.7 24.4 1.0 OD2 A:ASP108 3.8 18.4 1.0 CE1 A:HIS41 3.9 22.0 1.0 OE1 A:GLU80 4.0 28.8 1.0 O3P A:TMP303 4.0 28.6 1.0 CG A:GLU80 4.1 25.5 1.0 O A:HOH441 4.1 35.3 1.0 O5' A:TMP303 4.1 29.6 1.0 O A:HOH451 4.2 28.6 1.0 O A:HOH484 4.3 29.3 1.0 OE1 A:GLU119 4.3 25.1 1.0 CB A:GLU80 4.3 24.5 1.0 O A:LEU106 4.3 22.6 1.0 O A:PRO107 4.4 20.0 1.0 C5' A:TMP303 4.4 33.8 1.0 NE2 A:HIS41 4.5 21.4 1.0 C A:PRO107 4.5 21.2 1.0 CB A:ASP108 4.5 21.2 1.0 CA A:ASP108 4.5 20.6 1.0 O1P A:TMP303 4.5 26.8 1.0 N A:ASP108 4.6 20.0 1.0 OE2 A:GLU119 4.6 26.9 1.0 O A:HOH412 4.7 46.2 1.0 CD A:GLU119 4.9 27.1 1.0 CA A:GLU80 4.9 23.0 1.0 ND1 A:HIS41 4.9 21.7 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