Magnesium in PDB 4avq: Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease, PDB code: 4avq 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)	49.13 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	263.630, 66.240, 66.320, 90.00, 95.98, 90.00
R / Rfree (%)	23.457 / 28.386

The structure of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Magnesium atom in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease (pdb code 4avq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease, PDB code: 4avq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:37.1 occ:1.00 OD1 A:ASP108 2.2 23.4 1.0 O A:HOH2026 2.3 26.0 1.0 O A:HOH2021 2.4 44.1 1.0 OE1 A:GLU80 2.4 40.2 1.0 O A:HOH2020 2.5 25.6 1.0 O A:HOH2011 2.7 34.0 1.0 CG A:ASP108 3.3 21.0 1.0 CD A:GLU80 3.6 33.8 1.0 OD2 A:ASP108 3.9 26.6 1.0 MN A:MN901 3.9 42.2 1.0 O A:LEU106 4.0 22.7 1.0 NE2 A:HIS41 4.0 25.2 1.0 C A:PRO107 4.2 21.9 1.0 O A:PRO107 4.3 23.0 1.0 CA A:ASP108 4.3 21.2 1.0 CB A:ASP108 4.3 20.6 1.0 OE2 A:GLU80 4.3 42.1 1.0 N A:ASP108 4.4 19.8 1.0 CB A:GLU80 4.4 29.6 1.0 OE1 A:GLU119 4.4 30.9 1.0 CG A:GLU80 4.4 31.4 1.0 OE2 A:GLU119 4.7 28.8 1.0 CE1 A:HIS41 4.8 29.6 1.0 CA A:PRO107 4.8 23.1 1.0 CA A:GLU80 4.9 26.3 1.0 C A:LEU106 5.0 25.3 1.0 CD2 A:HIS41 5.0 26.0 1.0

Magnesium binding site 2 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:32.0 occ:1.00 OD1 B:ASP108 2.1 23.2 1.0 O B:HOH2012 2.3 22.1 1.0 OE1 B:GLU80 2.3 42.5 1.0 O B:HOH2033 2.4 40.4 1.0 O B:HOH2024 2.4 31.2 1.0 CG B:ASP108 3.2 23.7 1.0 O B:HOH2011 3.4 45.8 1.0 CD B:GLU80 3.5 41.5 1.0 OD2 B:ASP108 3.8 22.4 1.0 MN B:MN901 3.9 42.1 1.0 CE1 B:HIS41 3.9 26.2 1.0 O B:PRO107 4.1 23.6 1.0 CB B:ASP108 4.3 22.2 1.0 CA B:ASP108 4.3 22.6 1.0 C B:PRO107 4.3 25.3 1.0 OE2 B:GLU80 4.3 42.6 1.0 O B:LEU106 4.4 30.6 1.0 CG B:GLU80 4.4 37.5 1.0 CB B:GLU80 4.4 33.4 1.0 N B:ASP108 4.5 24.4 1.0 NE2 B:HIS41 4.6 25.8 1.0 OE1 B:GLU119 4.7 40.2 1.0 OE2 B:GLU119 4.7 34.7 1.0 CA B:GLU80 4.8 30.5 1.0 ND1 B:HIS41 4.9 25.5 1.0 O B:HOH2023 5.0 28.6 1.0

Magnesium binding site 3 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:35.9 occ:1.00 OE1 C:GLU80 2.1 43.4 1.0 OD1 C:ASP108 2.1 27.1 1.0 O C:HOH2006 2.4 22.4 1.0 O C:HOH2017 2.6 25.5 1.0 CG C:ASP108 3.3 26.2 1.0 CD C:GLU80 3.3 39.1 1.0 MN C:MN901 3.8 47.2 1.0 OD2 C:ASP108 3.9 26.7 1.0 NE2 C:HIS41 3.9 27.7 1.0 OE2 C:GLU80 4.2 47.3 1.0 CG C:GLU80 4.2 35.9 1.0 O C:PRO107 4.3 28.1 1.0 CB C:ASP108 4.3 24.0 1.0 CB C:GLU80 4.4 34.0 1.0 CA C:ASP108 4.4 23.0 1.0 C C:PRO107 4.4 26.6 1.0 O C:LEU106 4.4 24.0 1.0 N C:ASP108 4.5 24.0 1.0 OE1 C:GLU119 4.6 37.0 1.0 CE1 C:HIS41 4.7 26.6 1.0 OE2 C:GLU119 4.7 41.9 1.0 CA C:GLU80 4.8 30.8 1.0 CD2 C:HIS41 4.9 25.5 1.0

Magnesium binding site 4 out of 4 in the Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Influenza Strain PH1N1 2009 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:31.8 occ:1.00 OD1 D:ASP108 2.1 23.5 1.0 O D:HOH2022 2.3 26.7 1.0 O D:HOH2016 2.3 28.9 1.0 OE1 D:GLU80 2.3 41.5 1.0 O D:HOH2015 2.3 43.9 1.0 O D:HOH2010 2.4 29.9 1.0 CG D:ASP108 3.3 22.9 1.0 CD D:GLU80 3.5 37.7 1.0 NE2 D:HIS41 3.9 23.2 1.0 OD2 D:ASP108 3.9 23.8 1.0 MN D:MN901 4.0 47.3 1.0 O D:PRO107 4.2 21.3 1.0 CA D:ASP108 4.2 20.9 1.0 CG D:GLU80 4.3 35.4 1.0 O D:LEU106 4.3 22.5 1.0 CB D:ASP108 4.3 21.8 1.0 C D:PRO107 4.3 22.2 1.0 CB D:GLU80 4.4 31.8 1.0 OE2 D:GLU80 4.4 48.6 1.0 N D:ASP108 4.4 22.4 1.0 CA D:GLU80 4.7 27.9 1.0 CD2 D:HIS41 4.8 24.5 1.0 OE1 D:GLU119 4.8 32.9 1.0 CE1 D:HIS41 4.8 25.8 1.0 OE2 D:GLU119 4.9 31.2 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