Manganese in PDB 3hw6: Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn

The structure of Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn, PDB code: 3hw6 was solved by C.Zhao, Z.Lou, Y.Guo, M.Ma, Y.Chen, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.504, 60.211, 67.215, 96.06, 96.49, 109.66
R / Rfree (%)	24 / 28.9

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn (pdb code 3hw6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn, PDB code: 3hw6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


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 Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn257 b:37.6 occ:1.00 O A:ILE120 2.1 25.8 1.0 OE2 A:GLU119 2.2 29.4 1.0 OD2 A:ASP108 2.3 27.5 1.0 NE2 A:HIS41 2.4 18.2 1.0 O A:HOH259 2.6 29.2 1.0 CG A:ASP108 3.1 30.9 1.0 OD1 A:ASP108 3.1 32.8 1.0 CE1 A:HIS41 3.1 16.9 1.0 CD A:GLU119 3.3 31.0 1.0 C A:ILE120 3.3 26.1 1.0 CD2 A:HIS41 3.4 19.2 1.0 OE1 A:GLU119 3.7 31.2 1.0 MN A:MN258 3.8 41.4 1.0 N A:ILE120 3.8 27.4 1.0 NZ A:LYS134 3.8 26.0 1.0 CA A:ILE120 4.0 26.2 1.0 ND1 A:HIS41 4.3 16.6 1.0 N A:GLY121 4.3 25.8 1.0 CG A:HIS41 4.4 20.4 1.0 CG A:GLU119 4.5 31.8 1.0 CB A:ASP108 4.5 32.3 1.0 CB A:ILE120 4.6 25.3 1.0 OE2 A:GLU80 4.6 30.7 1.0 CA A:GLY121 4.7 26.6 1.0 C A:GLU119 4.7 29.0 1.0 CE A:LYS134 4.7 27.9 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


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 Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn258 b:41.4 occ:1.00 OD1 A:ASP108 1.9 32.8 1.0 OE2 A:GLU80 2.2 30.7 1.0 O A:HOH297 2.3 30.8 1.0 CG A:ASP108 3.1 30.9 1.0 CD A:GLU80 3.2 32.0 1.0 O A:HOH259 3.4 29.2 1.0 MN A:MN257 3.8 37.6 1.0 OD2 A:ASP108 3.8 27.5 1.0 O A:PRO107 3.9 36.4 1.0 OE1 A:GLU80 4.0 35.1 1.0 OE1 A:GLU119 4.0 31.2 1.0 CG A:GLU80 4.0 31.3 1.0 O A:LEU106 4.2 40.7 1.0 CE1 A:HIS41 4.2 16.9 1.0 CB A:ASP108 4.2 32.3 1.0 CB A:GLU80 4.2 31.1 1.0 CA A:ASP108 4.3 33.1 1.0 C A:PRO107 4.3 36.4 1.0 N A:ASP108 4.5 34.9 1.0 OE2 A:GLU119 4.5 29.4 1.0 CD A:GLU119 4.7 31.0 1.0 NE2 A:HIS41 4.7 18.2 1.0 CA A:GLU80 4.9 31.1 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


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 Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn257 b:37.1 occ:1.00 OD1 B:ASP108 1.8 35.4 1.0 OE2 B:GLU80 2.2 33.1 1.0 CG B:ASP108 3.0 33.3 1.0 OE1 B:GLU119 3.2 34.8 1.0 CD B:GLU80 3.2 34.8 1.0 OE1 B:GLU80 3.6 35.2 1.0 OD2 B:ASP108 3.6 30.4 1.0 CE1 B:HIS41 3.8 23.1 1.0 O B:PRO107 3.9 33.8 1.0 MN B:MN258 3.9 36.0 1.0 O B:LEU106 3.9 38.8 1.0 CB B:ASP108 4.2 32.5 1.0 CD B:GLU119 4.3 34.6 1.0 C B:PRO107 4.4 34.1 1.0 CA B:ASP108 4.4 32.3 1.0 CG B:GLU80 4.4 34.2 1.0 NE2 B:HIS41 4.6 25.7 1.0 CB B:GLU80 4.7 34.7 1.0 N B:ASP108 4.7 32.7 1.0 ND1 B:HIS41 4.7 27.6 1.0 OE2 B:GLU119 4.7 30.2 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn258 b:36.0 occ:1.00 O B:ILE120 2.0 31.7 1.0 NE2 B:HIS41 2.3 25.7 1.0 OD2 B:ASP108 2.3 30.4 1.0 OE2 B:GLU119 2.4 30.2 1.0 CE1 B:HIS41 2.8 23.1 1.0 NZ B:LYS134 2.9 36.9 1.0 C B:ILE120 3.1 32.2 1.0 CD B:GLU119 3.2 34.6 1.0 CG B:ASP108 3.2 33.3 1.0 OE1 B:GLU119 3.3 34.8 1.0 CD2 B:HIS41 3.4 24.4 1.0 OD1 B:ASP108 3.5 35.4 1.0 N B:ILE120 3.6 32.2 1.0 CE B:LYS134 3.8 41.6 1.0 CA B:ILE120 3.8 31.5 1.0 MN B:MN257 3.9 37.1 1.0 ND1 B:HIS41 4.0 27.6 1.0 N B:GLY121 4.2 32.1 1.0 CG B:HIS41 4.3 24.9 1.0 CB B:ILE120 4.3 31.0 1.0 C B:GLU119 4.4 32.9 1.0 CA B:GLY121 4.5 33.1 1.0 CG B:GLU119 4.6 33.8 1.0 CB B:ASP108 4.7 32.5 1.0 OE2 B:GLU80 4.7 33.1 1.0 CD B:LYS134 4.8 43.8 1.0 CA B:GLU119 4.9 32.6 1.0 O B:HOH262 4.9 5.0 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn257 b:33.5 occ:1.00 NE2 C:HIS41 2.0 37.1 1.0 O C:ILE120 2.3 26.9 1.0 OD2 C:ASP108 2.4 29.6 1.0 OE2 C:GLU119 2.6 28.2 1.0 CE1 C:HIS41 2.9 36.9 1.0 CD2 C:HIS41 3.1 33.8 1.0 CG C:ASP108 3.3 28.2 1.0 CD C:GLU119 3.3 29.0 1.0 OE1 C:GLU119 3.5 28.2 1.0 OD1 C:ASP108 3.5 29.1 1.0 C C:ILE120 3.5 27.8 1.0 N C:ILE120 4.0 27.5 1.0 O C:HOH273 4.0 42.6 1.0 MN C:MN258 4.0 44.4 1.0 ND1 C:HIS41 4.1 35.2 1.0 CA C:ILE120 4.2 27.0 1.0 CG C:HIS41 4.2 34.3 1.0 NZ C:LYS134 4.2 57.7 1.0 CB C:ILE120 4.4 26.9 1.0 OE2 C:GLU80 4.4 29.6 1.0 N C:GLY121 4.6 28.7 1.0 CG C:GLU119 4.7 29.8 1.0 CB C:ASP108 4.7 27.0 1.0 O C:HOH264 4.7 18.7 1.0 C C:GLU119 4.8 27.7 1.0 CA C:GLY121 4.9 30.4 1.0 CA C:GLU119 5.0 28.0 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn258 b:44.4 occ:1.00 OE2 C:GLU80 1.6 29.6 1.0 OD1 C:ASP108 2.1 29.1 1.0 CD C:GLU80 2.8 32.3 1.0 CG C:ASP108 3.2 28.2 1.0 OE1 C:GLU80 3.6 32.3 1.0 OE1 C:GLU119 3.6 28.2 1.0 CG C:GLU80 3.7 33.3 1.0 CB C:GLU80 3.8 36.2 1.0 OD2 C:ASP108 3.8 29.6 1.0 MN C:MN257 4.0 33.5 1.0 O C:HOH273 4.0 42.6 1.0 C C:PRO107 4.1 30.6 1.0 O C:PRO107 4.2 30.5 1.0 CE1 C:HIS41 4.2 36.9 1.0 O C:LEU106 4.3 32.8 1.0 N C:ASP108 4.3 28.2 1.0 CA C:ASP108 4.3 27.4 1.0 CB C:ASP108 4.4 27.0 1.0 CD C:GLU119 4.5 29.0 1.0 CA C:GLU80 4.5 36.9 1.0 CA C:PRO107 4.7 31.1 1.0 NE2 C:HIS41 4.7 37.1 1.0 OE2 C:GLU119 4.9 28.2 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn257 b:45.2 occ:1.00 O D:ILE120 2.1 35.4 1.0 OE2 D:GLU119 2.2 40.4 1.0 OD2 D:ASP108 2.4 35.8 1.0 NE2 D:HIS41 2.7 35.1 1.0 O D:HOH259 3.0 22.4 1.0 CD D:GLU119 3.0 38.0 1.0 CG D:ASP108 3.1 39.5 1.0 OD1 D:ASP108 3.2 37.4 1.0 OE1 D:GLU119 3.2 38.7 1.0 C D:ILE120 3.2 35.6 1.0 CE1 D:HIS41 3.3 34.5 1.0 CD2 D:HIS41 3.6 32.6 1.0 MN D:MN258 3.6 55.4 1.0 N D:ILE120 3.7 36.0 1.0 CA D:ILE120 4.0 35.3 1.0 CE D:LYS134 4.1 52.1 1.0 N D:GLY121 4.3 36.6 1.0 ND1 D:HIS41 4.3 34.9 1.0 CG D:GLU119 4.4 37.0 1.0 C D:GLU119 4.5 36.0 1.0 CG D:HIS41 4.5 33.2 1.0 CB D:ILE120 4.5 35.0 1.0 CB D:ASP108 4.6 41.1 1.0 CA D:GLY121 4.6 37.7 1.0 OE1 D:GLU80 4.7 45.0 1.0 CD D:LYS134 4.7 51.6 1.0 CB D:GLU119 4.7 36.2 1.0 CA D:GLU119 4.7 36.2 1.0 NZ D:LYS134 4.9 53.4 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Avian Influenza Virus PA_N in Complex with Mn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn258 b:55.4 occ:1.00 OE1 D:GLU80 2.3 45.0 1.0 OD1 D:ASP108 2.3 37.4 1.0 OE2 D:GLU80 2.6 44.7 1.0 CD D:GLU80 2.8 45.7 1.0 OE1 D:GLU119 2.9 38.7 1.0 O D:HOH259 3.0 22.4 1.0 CG D:ASP108 3.4 39.5 1.0 MN D:MN257 3.6 45.2 1.0 O D:LEU106 3.8 49.8 1.0 OD2 D:ASP108 4.0 35.8 1.0 CD D:GLU119 4.0 38.0 1.0 C D:PRO107 4.1 46.0 1.0 CE1 D:HIS41 4.1 34.5 1.0 O D:PRO107 4.2 46.1 1.0 CG D:GLU80 4.2 44.8 1.0 N D:ASP108 4.2 43.8 1.0 OE2 D:GLU119 4.3 40.4 1.0 CA D:ASP108 4.4 42.4 1.0 CB D:ASP108 4.5 41.1 1.0 NE2 D:HIS41 4.6 35.1 1.0 CA D:PRO107 4.6 47.6 1.0 C D:LEU106 4.8 50.2 1.0 CB D:GLU80 5.0 46.4 1.0

C.Zhao, Z.Lou, Y.Guo, M.Ma, Y.Chen, S.Liang, L.Zhang, S.Chen, X.Li, Y.Liu, M.Bartlam, Z.Rao. Nucleoside Monophosphate Complex Structures of the Endonuclease Domain From the Influenza Virus Polymerase Pa Subunit Reveal the Substrate Binding Site Inside the Catalytic Center J.Virol. V. 83 9024 2009.
ISSN: ISSN 0022-538X
PubMed: 19587036
DOI: 10.1128/JVI.00911-09