Manganese in PDB 5d9j: 2009 H1N1 Pa Endonuclease Mutant F105S in Complex with L-742,001

The structure of 2009 H1N1 Pa Endonuclease Mutant F105S in Complex with L-742,001, PDB code: 5d9j 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)	35.41 / 1.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.585, 60.585, 95.980, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 23

The structure of 2009 H1N1 Pa Endonuclease Mutant F105S 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 F105S in Complex with L-742,001 (pdb code 5d9j). 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 F105S in Complex with L-742,001, PDB code: 5d9j:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2009 H1N1 Pa Endonuclease Mutant F105S 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 F105S in Complex with L-742,001 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:24.1 occ:1.00 O25 A:0N8203 1.9 26.2 1.0 OD2 A:ASP89 2.0 25.9 1.0 O28 A:0N8203 2.2 23.9 1.0 OE2 A:GLU100 2.2 29.5 1.0 O A:ILE101 2.2 25.4 1.0 NE2 A:HIS41 2.3 29.1 1.0 C24 A:0N8203 2.9 28.2 1.0 C23 A:0N8203 3.0 24.4 1.0 CG A:ASP89 3.1 25.7 1.0 CE1 A:HIS41 3.2 28.8 1.0 CD A:GLU100 3.2 29.0 1.0 CD2 A:HIS41 3.3 25.8 1.0 OD1 A:ASP89 3.3 26.1 1.0 C A:ILE101 3.4 27.3 1.0 MN A:MN202 3.7 26.9 1.0 OE1 A:GLU100 3.8 29.0 1.0 N A:ILE101 3.8 26.9 1.0 O A:HOH333 3.9 24.7 1.0 CA A:ILE101 4.0 27.2 1.0 O26 A:0N8203 4.1 31.5 1.0 CB A:ILE101 4.3 27.7 1.0 ND1 A:HIS41 4.3 26.6 1.0 C22 A:0N8203 4.4 27.8 1.0 O A:HOH329 4.4 28.4 1.0 CG A:HIS41 4.4 26.6 1.0 N A:GLY102 4.4 24.8 1.0 CG A:GLU100 4.5 28.0 1.0 NZ A:LYS115 4.5 40.8 1.0 CB A:ASP89 4.5 26.4 1.0 CA A:GLY102 4.6 23.9 1.0 OE2 A:GLU61 4.7 30.5 1.0 C A:GLU100 4.8 29.4 1.0 O27 A:0N8203 4.9 31.2 1.0 CG2 A:ILE101 5.0 28.1 1.0

Manganese binding site 2 out of 2 in the 2009 H1N1 Pa Endonuclease Mutant F105S 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 F105S in Complex with L-742,001 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:26.9 occ:1.00 O A:HOH333 2.0 24.7 1.0 O27 A:0N8203 2.0 31.2 1.0 OE2 A:GLU61 2.1 30.5 1.0 O28 A:0N8203 2.1 23.9 1.0 OD1 A:ASP89 2.2 26.1 1.0 O A:HOH313 2.2 25.1 1.0 C14 A:0N8203 3.0 31.1 1.0 C23 A:0N8203 3.1 24.4 1.0 CG A:ASP89 3.2 25.7 1.0 CD A:GLU61 3.2 29.6 1.0 C22 A:0N8203 3.5 27.8 1.0 OD2 A:ASP89 3.6 25.9 1.0 MN A:MN201 3.7 24.1 1.0 CE1 A:HIS41 3.8 28.8 1.0 O A:PRO88 4.1 26.9 1.0 OE1 A:GLU61 4.1 28.5 1.0 CG A:GLU61 4.1 29.0 1.0 O A:HOH357 4.2 28.8 1.0 NE2 A:HIS41 4.3 29.1 1.0 CB A:GLU61 4.3 27.8 1.0 CB A:ASP89 4.4 26.4 1.0 OE1 A:GLU100 4.4 29.0 1.0 C A:PRO88 4.4 27.2 1.0 O A:LEU87 4.4 29.9 1.0 C11 A:0N8203 4.5 41.6 1.0 C24 A:0N8203 4.5 28.2 1.0 CA A:ASP89 4.5 25.6 1.0 OE2 A:GLU100 4.5 29.5 1.0 N A:ASP89 4.5 24.8 1.0 C21 A:0N8203 4.6 51.0 1.0 O25 A:0N8203 4.6 26.2 1.0 C13 A:0N8203 4.8 47.0 1.0 C12 A:0N8203 4.8 42.4 1.0 CD A:GLU100 4.9 29.0 1.0 CA A:GLU61 5.0 27.8 1.0 ND1 A:HIS41 5.0 26.6 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