Manganese in PDB 5d8u: 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with L-742,001

The structure of 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with L-742,001, PDB code: 5d8u 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)	46.00 / 2.29
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.881, 89.881, 134.148, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.1

The structure of 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with L-742,001 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with L-742,001 (pdb code 5d8u). 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 Mutant E119D in Complex with L-742,001, PDB code: 5d8u:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with L-742,001


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 L-742,001 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:51.7 occ:1.00 O A:ILE120 2.1 51.3 1.0 NE2 A:HIS41 2.2 53.1 1.0 O28 A:0N8203 2.2 62.1 1.0 O26 A:0N8203 2.2 61.9 1.0 OD2 A:ASP108 2.2 51.5 1.0 OD1 A:ASP119 2.3 70.6 1.0 CE1 A:HIS41 2.9 51.7 1.0 C24 A:0N8203 3.0 67.8 1.0 C23 A:0N8203 3.0 68.0 1.0 CG A:ASP108 3.1 50.8 1.0 C A:ILE120 3.2 54.1 1.0 CD2 A:HIS41 3.3 54.7 1.0 OD1 A:ASP108 3.4 50.2 1.0 CG A:ASP119 3.4 68.7 1.0 N A:ILE120 3.6 54.0 1.0 MN A:MN202 3.7 60.8 1.0 NZ A:LYS134 3.7 88.0 1.0 OD2 A:ASP119 3.9 83.7 1.0 CA A:ILE120 3.9 55.6 1.0 O A:HOH301 4.0 39.3 1.0 ND1 A:HIS41 4.1 51.1 1.0 O25 A:0N8203 4.2 68.7 1.0 C A:ASP119 4.2 58.5 1.0 CG A:HIS41 4.3 51.7 1.0 N A:GLY121 4.3 56.5 1.0 O A:HOH304 4.4 42.4 1.0 C22 A:0N8203 4.4 70.7 1.0 CB A:ILE120 4.4 57.1 1.0 CA A:ASP119 4.5 57.9 1.0 CB A:ASP108 4.5 50.4 1.0 CB A:ASP119 4.5 61.9 1.0 CA A:GLY121 4.7 54.6 1.0 CE A:LYS134 4.8 88.5 1.0 OE1 A:GLU80 4.8 66.9 1.0 O A:ASP119 4.9 59.7 1.0 SG A:CYS45 4.9 53.2 1.0

Manganese binding site 2 out of 2 in the 2009 H1N1 Pa Endonuclease Mutant E119D in Complex with L-742,001


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 Mutant E119D in Complex with L-742,001 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:60.8 occ:1.00 O28 A:0N8203 2.1 62.1 1.0 O27 A:0N8203 2.2 80.5 1.0 OD1 A:ASP108 2.2 50.2 1.0 O A:HOH301 2.2 39.3 1.0 O A:HOH302 2.3 47.1 1.0 OE1 A:GLU80 2.4 66.9 1.0 C14 A:0N8203 3.1 81.3 1.0 C23 A:0N8203 3.1 68.0 1.0 CG A:ASP108 3.3 50.8 1.0 C22 A:0N8203 3.4 70.7 1.0 CD A:GLU80 3.5 64.3 1.0 OD2 A:ASP108 3.7 51.5 1.0 MN A:MN201 3.7 51.7 1.0 CE1 A:HIS41 3.8 51.7 1.0 O A:LEU106 4.1 59.0 1.0 O A:PRO107 4.3 52.9 1.0 C A:PRO107 4.4 54.5 1.0 OE2 A:GLU80 4.4 72.0 1.0 CB A:ASP108 4.4 50.4 1.0 N A:ASP108 4.4 53.6 1.0 CG A:GLU80 4.4 58.5 1.0 NE2 A:HIS41 4.4 53.1 1.0 CA A:ASP108 4.5 51.5 1.0 C24 A:0N8203 4.5 67.8 1.0 C11 A:0N8203 4.5 91.3 1.0 C17 A:0N8203 4.6 99.4 1.0 OD1 A:ASP119 4.7 70.6 1.0 CB A:GLU80 4.7 55.4 1.0 OD2 A:ASP119 4.8 83.7 1.0 O26 A:0N8203 4.8 61.9 1.0 ND1 A:HIS41 4.8 51.1 1.0 C15 A:0N8203 4.8 94.1 1.0 C A:LEU106 4.9 60.9 1.0 CG A:ASP119 5.0 68.7 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