Manganese in PDB 2w69: Influenza Polymerase Fragment

The structure of Influenza Polymerase Fragment, PDB code: 2w69 was solved by A.Dias, D.Bouvier, T.Crepin, A.A.Mccarthy, D.J.Hart, F.Baudin, S.Cusack, R.W.H.Ruigrok, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.81 / 2.05
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.130, 67.130, 302.950, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.8

The binding sites of Manganese atom in the Influenza Polymerase Fragment (pdb code 2w69). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Influenza Polymerase Fragment, PDB code: 2w69:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Influenza Polymerase Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza Polymerase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:34.8 occ:0.80 OE2 D:GLU59 2.1 51.5 1.0 OD1 A:ASP108 2.2 26.6 1.0 O A:HOH2065 2.3 24.9 1.0 O A:HOH2064 2.4 27.4 1.0 OE1 A:GLU80 2.4 27.8 1.0 CD D:GLU59 3.2 49.5 1.0 CG A:ASP108 3.2 26.2 1.0 MN A:MN302 3.3 49.1 0.4 CD A:GLU80 3.5 26.2 1.0 CG D:GLU59 3.6 47.6 1.0 OD2 A:ASP108 3.8 27.0 1.0 CE1 A:HIS41 3.9 23.4 1.0 O A:HOH2038 4.0 35.5 1.0 O A:LEU106 4.2 30.5 1.0 CG A:GLU80 4.3 27.0 1.0 O A:PRO107 4.3 28.4 1.0 OE1 D:GLU59 4.3 49.8 1.0 OE2 A:GLU80 4.3 29.7 1.0 CB A:ASP108 4.4 23.9 1.0 OE2 A:GLU119 4.4 30.6 1.0 NE2 A:HIS41 4.4 25.8 1.0 CA A:ASP108 4.4 26.3 1.0 OE1 A:GLU119 4.4 33.9 1.0 C A:PRO107 4.5 28.4 1.0 CB A:GLU80 4.5 26.3 1.0 N A:ASP108 4.6 27.2 1.0 CD A:GLU119 4.9 32.4 1.0 OG D:SER60 4.9 44.2 1.0

Manganese binding site 2 out of 5 in the Influenza Polymerase Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza Polymerase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:49.1 occ:0.40 OE2 D:GLU59 1.8 51.5 1.0 OD2 A:ASP108 2.0 27.0 1.0 O A:ILE120 2.2 29.2 1.0 CD D:GLU59 2.4 49.5 1.0 OE1 D:GLU59 2.4 49.8 1.0 OE2 A:GLU119 2.5 30.6 1.0 CG A:ASP108 2.8 26.2 1.0 NE2 A:HIS41 2.9 25.8 1.0 OD1 A:ASP108 2.9 26.6 1.0 MN A:MN301 3.3 34.8 0.8 CD A:GLU119 3.3 32.4 1.0 C A:ILE120 3.3 28.0 1.0 CE1 A:HIS41 3.5 23.4 1.0 O A:HOH2064 3.6 27.4 1.0 N A:ILE120 3.6 28.1 1.0 OE1 A:GLU119 3.8 33.9 1.0 CG D:GLU59 3.8 47.6 1.0 CA A:ILE120 3.9 27.7 1.0 CD2 A:HIS41 4.0 23.4 1.0 O D:HOH2008 4.1 31.8 1.0 CB A:ASP108 4.2 23.9 1.0 NZ A:LYS134 4.2 37.3 1.0 CE A:LYS134 4.3 40.4 1.0 CG A:GLU119 4.4 32.0 1.0 CB A:ILE120 4.4 28.5 1.0 N A:GLY121 4.5 27.1 1.0 C A:GLU119 4.5 26.8 1.0 OE1 A:GLU80 4.7 27.8 1.0 CB D:GLU59 4.7 48.1 1.0 ND1 A:HIS41 4.7 23.1 1.0 CA A:GLU119 4.9 29.5 1.0 CA A:GLY121 4.9 27.8 1.0

Manganese binding site 3 out of 5 in the Influenza Polymerase Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Influenza Polymerase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:51.4 occ:0.50 OD1 B:ASP108 2.4 22.6 1.0 O B:HOH2069 2.7 33.5 1.0 OE2 A:GLU59 2.8 28.2 1.0 CG B:ASP108 3.2 22.3 1.0 OD2 B:ASP108 3.3 24.6 1.0 O B:HOH2072 3.4 28.6 1.0 O B:HOH2043 3.4 27.8 1.0 OE1 B:GLU80 3.4 37.3 1.0 O B:HOH2046 3.5 30.9 1.0 O B:LEU106 3.7 23.2 1.0 CD A:GLU59 3.7 31.3 1.0 CE1 B:HIS41 3.7 20.9 1.0 CG A:GLU59 3.8 28.4 1.0 NE2 B:HIS41 4.0 22.4 1.0 CB A:GLU59 4.1 27.5 1.0 CB B:ASP108 4.5 23.5 1.0 C B:PRO107 4.5 23.8 1.0 N B:ASP108 4.5 23.4 1.0 O B:PRO107 4.6 22.2 1.0 CD B:GLU80 4.6 35.5 1.0 CA B:ASP108 4.7 23.7 1.0 C B:LEU106 4.8 24.4 1.0 CG B:GLU119 4.8 33.4 1.0 ND1 B:HIS41 4.9 19.1 1.0 OE1 A:GLU59 4.9 34.1 1.0 CA B:PRO107 4.9 23.5 1.0

Manganese binding site 4 out of 5 in the Influenza Polymerase Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Influenza Polymerase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:60.2 occ:0.50 O D:HOH2013 2.1 34.4 1.0 OD1 D:ASP108 2.3 38.1 1.0 OE1 D:GLU80 2.7 46.1 1.0 CG D:ASP108 3.4 38.2 1.0 CD D:GLU80 3.6 43.6 1.0 MN D:MN302 3.9 49.2 0.4 O D:PRO107 3.9 33.9 1.0 CE1 D:HIS41 4.0 30.1 1.0 O D:LEU106 4.0 45.6 1.0 O D:HOH2009 4.1 43.4 1.0 OD2 D:ASP108 4.1 37.9 1.0 CG D:GLU80 4.2 42.4 1.0 C D:PRO107 4.2 37.5 1.0 CB D:GLU80 4.3 41.8 1.0 CA D:ASP108 4.4 37.4 1.0 OE2 D:GLU80 4.4 44.0 1.0 N D:ASP108 4.4 38.0 1.0 CB D:ASP108 4.5 37.5 1.0 OE2 D:GLU119 4.6 43.0 1.0 NE2 D:HIS41 4.6 31.7 1.0 OE1 D:GLU119 4.7 49.4 1.0 C D:LEU106 4.8 43.3 1.0 CA D:GLU80 4.9 39.9 1.0 CA D:PRO107 4.9 40.4 1.0 ND1 D:HIS41 5.0 27.9 1.0

Manganese binding site 5 out of 5 in the Influenza Polymerase Fragment


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Influenza Polymerase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:49.2 occ:0.40 O D:ILE120 2.1 40.5 1.0 OD2 D:ASP108 2.4 37.9 1.0 NE2 D:HIS41 2.5 31.7 1.0 OE2 D:GLU119 3.0 43.0 1.0 CG D:ASP108 3.1 38.2 1.0 OD1 D:ASP108 3.2 38.1 1.0 CE1 D:HIS41 3.2 30.1 1.0 C D:ILE120 3.3 40.1 1.0 CD2 D:HIS41 3.5 28.8 1.0 N D:ILE120 3.7 39.7 1.0 CD D:GLU119 3.8 46.1 1.0 MN D:MN301 3.9 60.2 0.5 CA D:ILE120 4.0 40.5 1.0 ND1 D:HIS41 4.3 27.9 1.0 NZ D:LYS134 4.3 51.2 1.0 OE1 D:GLU119 4.3 49.4 1.0 N D:GLY121 4.4 41.1 1.0 CE D:LYS134 4.4 52.4 1.0 CB D:ILE120 4.4 39.5 1.0 CG D:HIS41 4.5 28.6 1.0 CB D:ASP108 4.6 37.5 1.0 CA D:GLY121 4.6 39.1 1.0 CG D:GLU119 4.7 47.5 1.0 C D:GLU119 4.7 43.1 1.0 CG2 D:ILE120 5.0 39.2 1.0

A.Dias, D.Bouvier, T.Crepin, A.A.Mccarthy, D.J.Hart, F.Baudin, S.Cusack, R.W.H.Ruigrok. The Cap-Snatching Endonuclease of Influenza Virus Polymerase Resides in the Pa Subunit Nature V. 458 914 2009.
ISSN: ISSN 0028-0836
PubMed: 19194459
DOI: 10.1038/NATURE07745