Manganese in PDB 4awk: Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1, PDB code: 4awk was solved by E.Kowalinski, C.Zubieta, A.Wolkerstorfer, O.H.Szolar, R.W.Ruigrok, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.01 / 1.90
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.060, 75.060, 120.050, 90.00, 90.00, 120.00
R / Rfree (%)	20.84 / 23.568

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1 (pdb code 4awk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1, PDB code: 4awk:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn901 b:27.6 occ:1.00 O A:ILE120 2.0 27.6 1.0 OAO A:CI1801 2.1 32.7 1.0 OD2 A:ASP108 2.2 28.0 1.0 OE2 A:GLU119 2.2 28.9 1.0 NE2 A:HIS41 2.2 25.5 1.0 O14 A:CI1801 2.2 28.3 1.0 CE A:CI1801 2.8 34.7 1.0 CA A:CI1801 2.9 34.3 1.0 CG A:ASP108 3.0 25.8 1.0 CE1 A:HIS41 3.1 27.5 1.0 CD2 A:HIS41 3.2 26.9 1.0 C A:ILE120 3.2 26.4 1.0 CD A:GLU119 3.2 29.6 1.0 OD1 A:ASP108 3.3 25.3 1.0 N A:ILE120 3.7 25.2 1.0 MN A:MN902 3.7 33.8 1.0 OE1 A:GLU119 3.7 28.5 1.0 CA A:ILE120 3.9 26.8 1.0 O A:HOH2037 4.0 31.5 1.0 OAN A:CI1801 4.0 37.0 1.0 CB A:ILE120 4.1 27.0 1.0 CM A:CI1801 4.2 36.1 1.0 ND1 A:HIS41 4.2 26.6 1.0 CG A:HIS41 4.3 26.3 1.0 N A:GLY121 4.3 28.6 1.0 CG A:GLU119 4.3 29.3 1.0 O A:HOH2047 4.4 26.4 1.0 CB A:ASP108 4.4 24.9 1.0 NZ A:LYS134 4.6 46.7 1.0 CE A:LYS134 4.6 44.7 1.0 CA A:GLY121 4.6 28.1 1.0 C A:GLU119 4.6 26.8 1.0 OE2 A:GLU80 4.8 31.8 1.0 CG2 A:ILE120 4.9 27.6 1.0 O13 A:CI1801 5.0 35.8 1.0

Manganese binding site 2 out of 2 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease in Complex with Diketo Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn902 b:33.8 occ:1.00 O14 A:CI1801 2.0 28.3 1.0 OD1 A:ASP108 2.1 25.3 1.0 O13 A:CI1801 2.1 35.8 1.0 O A:HOH2037 2.2 31.5 1.0 O A:HOH2021 2.2 34.0 1.0 OE2 A:GLU80 2.2 31.8 1.0 CB A:CI1801 3.0 39.6 1.0 CA A:CI1801 3.1 34.3 1.0 CG A:ASP108 3.2 25.8 1.0 CD A:GLU80 3.4 32.7 1.0 CM A:CI1801 3.4 36.1 1.0 OD2 A:ASP108 3.7 28.0 1.0 MN A:MN901 3.7 27.6 1.0 CE1 A:HIS41 3.8 27.5 1.0 O A:HOH2020 4.1 41.7 1.0 OE1 A:GLU80 4.2 38.7 1.0 CG A:GLU80 4.2 33.0 1.0 NE2 A:HIS41 4.3 25.5 1.0 O A:PRO107 4.3 26.9 1.0 OE1 A:GLU119 4.3 28.5 1.0 CB A:ASP108 4.4 24.9 1.0 CF A:CI1801 4.4 46.5 1.0 CE A:CI1801 4.4 34.7 1.0 O A:LEU106 4.4 26.3 1.0 C A:PRO107 4.4 26.7 1.0 CA A:ASP108 4.4 26.1 1.0 CB A:GLU80 4.5 30.1 1.0 OE2 A:GLU119 4.5 28.9 1.0 N A:ASP108 4.6 24.6 1.0 O31 A:CI1801 4.7 56.8 0.6 CH A:CI1801 4.8 47.9 1.0 CO A:CI1801 4.8 50.2 1.0 OAO A:CI1801 4.8 32.7 1.0 ND1 A:HIS41 4.9 26.6 1.0 CD A:GLU119 4.9 29.6 1.0

E.Kowalinski, C.Zubieta, A.Wolkerstorfer, O.H.Szolar, R.W.Ruigrok, S.Cusack. Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza PH1N1 (2009) Polymerase. Plos Pathog. V. 8 2831 2012.
ISSN: ISSN 1553-7366
PubMed: 22876177
DOI: 10.1371/JOURNAL.PPAT.1002831