Manganese in PDB 5i13: Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0

The structure of Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0, PDB code: 5i13 was solved by S.Fudo, N.Yamamoto, M.Nukaga, T.Odagiri, M.Tashiro, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.96 / 2.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.580, 66.580, 128.314, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.3

The structure of Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0 (pdb code 5i13). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0, PDB code: 5i13:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:27.5 occ:1.00 OE2 A:GLU119 2.0 28.8 1.0 OAH A:4P9305 2.1 31.0 1.0 OD2 A:ASP108 2.1 25.9 1.0 O A:ILE120 2.1 28.5 1.0 OAG A:4P9305 2.2 39.8 1.0 NE2 A:HIS41 2.2 28.4 1.0 CAF A:4P9305 2.8 39.4 1.0 CAE A:4P9305 2.9 33.0 1.0 CE1 A:HIS41 3.0 23.1 1.0 CG A:ASP108 3.0 27.9 1.0 CD A:GLU119 3.1 31.9 1.0 C A:ILE120 3.2 24.9 1.0 OD1 A:ASP108 3.3 28.6 1.0 CD2 A:HIS41 3.3 28.7 1.0 N A:ILE120 3.6 26.9 1.0 OE1 A:GLU119 3.8 28.3 1.0 MN A:MN302 3.8 31.0 1.0 CA A:ILE120 3.9 23.0 1.0 O A:HOH414 3.9 26.8 1.0 NZ A:LYS134 4.0 42.5 1.0 CAA A:4P9305 4.1 62.3 1.0 ND1 A:HIS41 4.2 22.6 1.0 CB A:ILE120 4.2 30.2 1.0 CAD A:4P9305 4.2 61.8 1.0 CG A:GLU119 4.3 26.3 1.0 N A:GLY121 4.4 29.0 1.0 CG A:HIS41 4.4 28.6 1.0 CB A:ASP108 4.4 24.3 1.0 C A:GLU119 4.6 30.0 1.0 OAI A:4P9305 4.6 49.4 1.0 CA A:GLY121 4.7 32.5 1.0 OE1 A:GLU80 4.7 25.7 1.0 CE A:LYS134 4.9 37.9 1.0 CA A:GLU119 5.0 30.1 1.0

Manganese binding site 2 out of 2 in the Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Endonuclease Inhibitor 2 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:31.0 occ:1.00 O A:HOH414 1.9 26.8 1.0 OE1 A:GLU80 1.9 25.7 1.0 O A:HOH408 2.0 28.9 1.0 OD1 A:ASP108 2.1 28.6 1.0 OAH A:4P9305 2.2 31.0 1.0 OAI A:4P9305 2.4 49.4 1.0 CAF A:4P9305 3.1 39.4 1.0 CD A:GLU80 3.1 33.9 1.0 CAA A:4P9305 3.2 62.3 1.0 CG A:ASP108 3.2 27.9 1.0 OD2 A:ASP108 3.7 25.9 1.0 MN A:MN301 3.8 27.5 1.0 CE1 A:HIS41 4.0 23.1 1.0 OE2 A:GLU80 4.0 40.0 1.0 CG A:GLU80 4.0 32.6 1.0 O A:PRO107 4.2 27.2 1.0 O A:LEU106 4.2 31.2 1.0 OE1 A:GLU119 4.3 28.3 1.0 CB A:GLU80 4.3 34.6 1.0 CB A:ASP108 4.4 24.3 1.0 OE2 A:GLU119 4.4 28.8 1.0 C A:PRO107 4.4 30.4 1.0 CAE A:4P9305 4.4 33.0 1.0 CA A:ASP108 4.5 27.3 1.0 CAB A:4P9305 4.5 75.3 1.0 NE2 A:HIS41 4.5 28.4 1.0 N A:ASP108 4.6 24.8 1.0 CD A:GLU119 4.8 31.9 1.0 OAG A:4P9305 4.9 39.8 1.0 CA A:GLU80 4.9 33.0 1.0

S.Fudo, N.Yamamoto, M.Nukaga, T.Odagiri, M.Tashiro, T.Hoshino. Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit Biochemistry V. 55 2646 2016.
ISSN: ISSN 0006-2960
PubMed: 27088785
DOI: 10.1021/ACS.BIOCHEM.5B01087