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

The structure of 2009 H1N1 Pa Endonuclease in Complex with L-742,001, PDB code: 5cgv 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 / 2.17
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.899, 73.899, 127.457, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 28.2

The structure of 2009 H1N1 Pa Endonuclease 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 in Complex with L-742,001 (pdb code 5cgv). 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 L-742,001, PDB code: 5cgv:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2009 H1N1 Pa Endonuclease 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 in Complex with L-742,001 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:49.3 occ:1.00 OD2 A:ASP108 2.3 23.9 1.0 O A:ILE120 2.3 28.1 1.0 O26 A:0N8303 2.3 28.3 1.0 NE2 A:HIS41 2.3 25.6 1.0 O28 A:0N8303 2.3 30.6 1.0 OE2 A:GLU119 2.3 30.7 1.0 C24 A:0N8303 2.9 27.8 1.0 C23 A:0N8303 3.0 29.7 1.0 CE1 A:HIS41 3.1 24.9 1.0 CG A:ASP108 3.1 25.4 1.0 CD A:GLU119 3.2 31.1 1.0 OD1 A:ASP108 3.2 25.4 1.0 C A:ILE120 3.4 27.4 1.0 CD2 A:HIS41 3.4 25.4 1.0 OE1 A:GLU119 3.5 31.6 1.0 MN A:MN302 3.6 59.1 1.0 N A:ILE120 3.7 29.8 1.0 CA A:ILE120 4.0 28.4 1.0 O A:HOH401 4.1 22.8 1.0 O25 A:0N8303 4.1 27.3 1.0 ND1 A:HIS41 4.3 26.2 1.0 C22 A:0N8303 4.3 31.7 1.0 CB A:ILE120 4.3 28.2 1.0 N A:GLY121 4.4 28.8 1.0 CG A:HIS41 4.4 25.5 1.0 CG A:GLU119 4.4 32.1 1.0 CB A:ASP108 4.5 26.5 1.0 O A:HOH402 4.5 23.6 1.0 OE2 A:GLU80 4.6 25.6 1.0 CA A:GLY121 4.7 27.5 1.0 C A:GLU119 4.7 30.4 1.0 CE A:LYS134 4.8 44.0 1.0 SG A:CYS45 4.8 25.9 1.0 CA A:GLU119 5.0 29.9 1.0

Manganese binding site 2 out of 2 in the 2009 H1N1 Pa Endonuclease 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 in Complex with L-742,001 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:59.1 occ:1.00 O28 A:0N8303 2.1 30.6 1.0 OD1 A:ASP108 2.1 25.4 1.0 O A:HOH401 2.1 22.8 1.0 O27 A:0N8303 2.2 34.3 1.0 OE2 A:GLU80 2.3 25.6 1.0 O A:HOH428 2.4 21.1 1.0 CG A:ASP108 3.0 25.4 1.0 C14 A:0N8303 3.1 34.8 1.0 C23 A:0N8303 3.2 29.7 1.0 CD A:GLU80 3.3 24.5 1.0 OD2 A:ASP108 3.5 23.9 1.0 C22 A:0N8303 3.5 31.7 1.0 MN A:MN301 3.6 49.3 1.0 O A:PRO107 3.9 22.2 1.0 OE1 A:GLU119 3.9 31.6 1.0 CE1 A:HIS41 4.0 24.9 1.0 OE1 A:GLU80 4.0 23.3 1.0 C A:PRO107 4.1 25.3 1.0 O A:HOH425 4.1 19.3 1.0 CG A:GLU80 4.1 25.4 1.0 CB A:ASP108 4.1 26.5 1.0 O A:HOH420 4.2 39.7 1.0 CA A:ASP108 4.2 26.4 1.0 O A:LEU106 4.2 28.7 1.0 CB A:GLU80 4.2 24.8 1.0 N A:ASP108 4.2 26.4 1.0 C24 A:0N8303 4.5 27.8 1.0 NE2 A:HIS41 4.5 25.6 1.0 C11 A:0N8303 4.5 37.6 1.0 C17 A:0N8303 4.6 39.7 1.0 OE2 A:GLU119 4.6 30.7 1.0 CD A:GLU119 4.7 31.1 1.0 CA A:GLU80 4.8 25.2 1.0 CA A:PRO107 4.8 26.9 1.0 C15 A:0N8303 4.8 38.1 1.0 C A:LEU106 4.9 28.7 1.0 O26 A:0N8303 4.9 28.3 1.0 C12 A:0N8303 4.9 35.9 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