Manganese in PDB 4nfz: Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10

The structure of Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10, PDB code: 4nfz was solved by B.Tefsen, G.Lu, Y.Zhu, J.Haywood, L.Zhao, T.Deng, J.Qi, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.80 / 2.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.300, 74.300, 401.159, 90.00, 90.00, 120.00
R / Rfree (%)	24 / 27.8

The binding sites of Manganese atom in the Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10 (pdb code 4nfz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10, PDB code: 4nfz:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:43.9 occ:1.00 OE2 A:GLU119 2.1 57.1 1.0 O A:ILE120 2.2 43.8 1.0 NE2 A:HIS41 2.2 41.8 1.0 OD2 A:ASP108 2.2 36.6 1.0 CD2 A:HIS41 3.0 31.6 1.0 CE1 A:HIS41 3.0 40.0 1.0 CG A:ASP108 3.2 40.2 1.0 CD A:GLU119 3.4 66.0 1.0 C A:ILE120 3.4 38.1 1.0 OD1 A:ASP108 3.4 43.1 1.0 CG A:HIS41 4.0 32.1 1.0 ND1 A:HIS41 4.0 38.4 1.0 OE1 A:GLU119 4.1 60.1 1.0 N A:ILE120 4.2 38.2 1.0 CA A:ILE120 4.3 36.0 1.0 CE A:LYS134 4.4 60.5 1.0 N A:GLY121 4.4 46.3 1.0 CG A:GLU119 4.4 49.0 1.0 CA A:GLY121 4.5 50.6 1.0 CB A:ASP108 4.7 30.1 1.0 CB A:ILE120 4.9 38.6 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:45.6 occ:1.00 OE2 B:GLU119 2.1 53.6 1.0 O B:ILE120 2.2 53.4 1.0 NE2 B:HIS41 2.2 43.7 1.0 OD2 B:ASP108 2.2 38.0 1.0 CD2 B:HIS41 2.9 35.9 1.0 CE1 B:HIS41 3.0 38.4 1.0 CG B:ASP108 3.2 42.6 1.0 CD B:GLU119 3.4 64.7 1.0 C B:ILE120 3.4 49.4 1.0 OD1 B:ASP108 3.4 44.2 1.0 CG B:HIS41 4.0 34.9 1.0 ND1 B:HIS41 4.0 37.6 1.0 OE1 B:GLU119 4.1 58.4 1.0 N B:ILE120 4.3 46.8 1.0 CA B:ILE120 4.4 44.6 1.0 CE B:LYS134 4.4 62.9 1.0 N B:GLY121 4.4 36.6 1.0 CG B:GLU119 4.4 49.3 1.0 CA B:GLY121 4.5 43.4 1.0 CB B:ASP108 4.7 35.9 1.0 CB B:ILE120 4.9 42.6 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Polymerase Subunit Pa N-Terminal Endonuclease Domain From Bat-Derived Influenza Virus H17N10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn300 b:51.1 occ:1.00 OE2 C:GLU119 2.1 60.4 1.0 O C:ILE120 2.2 56.8 1.0 OD2 C:ASP108 2.2 45.5 1.0 NE2 C:HIS41 2.2 43.8 1.0 CD2 C:HIS41 3.0 36.7 1.0 CE1 C:HIS41 3.0 41.0 1.0 CG C:ASP108 3.2 50.1 1.0 CD C:GLU119 3.4 67.3 1.0 OD1 C:ASP108 3.4 52.7 1.0 C C:ILE120 3.4 51.5 1.0 CG C:HIS41 4.0 38.4 1.0 ND1 C:HIS41 4.0 41.5 1.0 OE1 C:GLU119 4.1 58.6 1.0 N C:ILE120 4.2 48.9 1.0 CA C:ILE120 4.3 49.2 1.0 CE C:LYS134 4.4 60.2 1.0 N C:GLY121 4.4 46.0 1.0 CG C:GLU119 4.4 54.8 1.0 CA C:GLY121 4.5 53.8 1.0 CB C:ASP108 4.6 42.0 1.0 CB C:ILE120 4.9 46.8 1.0 OE1 C:GLU80 5.0 47.1 1.0

B.Tefsen, G.Lu, Y.Zhu, J.Haywood, L.Zhao, T.Deng, J.Qi, G.F.Gao. The N-Terminal Domain of Pa From Bat-Derived Influenza-Like Virus H17N10 Has Endonuclease Activity J.Virol. V. 88 1935 2014.
ISSN: ISSN 0022-538X
PubMed: 24284327
DOI: 10.1128/JVI.03270-13