Manganese in PDB 5fdg: Endonuclease Inhibitor 3 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0

The structure of Endonuclease Inhibitor 3 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0, PDB code: 5fdg 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)	37.76 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.438, 66.438, 126.977, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.8

The structure of Endonuclease Inhibitor 3 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Endonuclease Inhibitor 3 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0 (pdb code 5fdg). 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 3 Bound to Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region at pH 7.0, PDB code: 5fdg:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Endonuclease Inhibitor 3 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 3 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:Mn202 b:21.1 occ:1.00 OE2 A:GLU104 2.0 24.2 1.0 OD2 A:ASP93 2.1 16.7 1.0 O A:ILE105 2.2 23.8 1.0 NE2 A:HIS46 2.2 21.5 1.0 O25 A:0N8204 2.2 23.5 1.0 O28 A:0N8204 2.4 26.4 1.0 C24 A:0N8204 2.8 28.7 1.0 C23 A:0N8204 2.9 28.7 1.0 CE1 A:HIS46 3.0 24.0 1.0 CG A:ASP93 3.0 21.2 1.0 CD A:GLU104 3.2 24.8 1.0 OD1 A:ASP93 3.2 17.9 1.0 CD2 A:HIS46 3.3 24.4 1.0 C A:ILE105 3.3 27.5 1.0 N A:ILE105 3.7 18.5 1.0 MN A:MN203 3.7 23.2 1.0 OE1 A:GLU104 3.8 21.2 1.0 O A:HOH346 3.8 26.2 1.0 O26 A:0N8204 4.0 43.1 1.0 CA A:ILE105 4.0 18.2 1.0 ND1 A:HIS46 4.2 17.1 1.0 O A:HOH308 4.3 21.4 1.0 CG A:GLU104 4.3 20.0 1.0 CB A:ILE105 4.3 21.6 1.0 CG A:HIS46 4.3 21.0 1.0 C22 A:0N8204 4.3 33.6 1.0 N A:GLY106 4.4 22.6 1.0 CB A:ASP93 4.4 18.3 1.0 CA A:GLY106 4.6 21.5 1.0 OE2 A:GLU65 4.6 23.2 1.0 C A:GLU104 4.7 25.0 1.0 CE A:LYS119 4.8 35.9 1.0 CA A:GLU104 5.0 21.9 1.0 O27 A:0N8204 5.0 28.5 1.0

Manganese binding site 2 out of 2 in the Endonuclease Inhibitor 3 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 3 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:Mn203 b:23.2 occ:1.00 O A:HOH346 1.9 26.2 1.0 OE2 A:GLU65 2.0 23.2 1.0 O28 A:0N8204 2.1 26.4 1.0 OD1 A:ASP93 2.2 17.9 1.0 O27 A:0N8204 2.2 28.5 1.0 O A:HOH331 2.3 23.2 1.0 CD A:GLU65 3.1 33.4 1.0 CG A:ASP93 3.2 21.2 1.0 C23 A:0N8204 3.2 28.7 1.0 C14 A:0N8204 3.4 49.3 1.0 OD2 A:ASP93 3.7 16.7 1.0 MN A:MN202 3.7 21.1 1.0 C22 A:0N8204 3.8 33.6 1.0 CE1 A:HIS46 3.8 24.0 1.0 O A:HOH320 3.9 37.1 1.0 OE1 A:GLU65 3.9 31.2 1.0 CG A:GLU65 4.1 23.2 1.0 O A:PRO92 4.1 21.7 1.0 CB A:GLU65 4.3 22.0 1.0 C1 A:0N8204 4.3 46.8 1.0 CB A:ASP93 4.3 18.3 1.0 CA A:ASP93 4.4 22.0 1.0 O A:LEU91 4.4 23.9 1.0 C A:PRO92 4.4 20.6 1.0 NE2 A:HIS46 4.4 21.5 1.0 OE1 A:GLU104 4.4 21.2 1.0 C6 A:0N8204 4.5 59.8 1.0 OE2 A:GLU104 4.5 24.2 1.0 N A:ASP93 4.5 18.9 1.0 C24 A:0N8204 4.5 28.7 1.0 C15 A:0N8204 4.6 42.3 1.0 C11 A:0N8204 4.7 43.9 1.0 CA A:GLU65 4.8 24.8 1.0 C17 A:0N8204 4.8 46.6 1.0 ND1 A:HIS46 4.8 17.1 1.0 O25 A:0N8204 4.9 23.5 1.0 CD A:GLU104 4.9 24.8 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