Manganese in PDB 6fs6: Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)

The structure of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa), PDB code: 6fs6 was solved by S.Cusack, V.Speranzini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.40 / 2.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	135.180, 75.690, 121.590, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.1

The structure of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) (pdb code 6fs6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa), PDB code: 6fs6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn901 b:50.4 occ:1.00 O A:ILE120 2.1 36.5 1.0 OD2 A:ASP108 2.1 40.8 1.0 O1 A:E4Z903 2.3 41.0 1.0 OE2 A:GLU119 2.3 35.4 1.0 NE2 A:HIS41 2.3 36.5 1.0 O2 A:E4Z903 2.4 41.7 1.0 C1 A:E4Z903 3.0 33.8 1.0 C5 A:E4Z903 3.0 34.5 1.0 CG A:ASP108 3.0 32.6 1.0 CE1 A:HIS41 3.2 40.9 1.0 C A:ILE120 3.2 37.7 1.0 CD2 A:HIS41 3.3 34.9 1.0 OD1 A:ASP108 3.3 42.5 1.0 CD A:GLU119 3.3 36.5 1.0 N A:ILE120 3.7 41.5 1.0 MN A:MN902 3.8 69.8 1.0 CA A:ILE120 3.9 35.6 1.0 OE1 A:GLU119 3.9 41.5 1.0 O A:HOH1001 3.9 34.5 1.0 NZ A:LYS134 4.2 69.4 1.0 CB A:ILE120 4.2 37.8 1.0 ND1 A:HIS41 4.3 38.1 1.0 C2 A:E4Z903 4.3 39.4 1.0 N A:GLY121 4.3 36.5 1.0 CG A:GLU119 4.3 38.9 1.0 CG A:HIS41 4.4 44.2 1.0 C4 A:E4Z903 4.4 37.9 1.0 CB A:ASP108 4.4 36.0 1.0 C A:GLU119 4.6 38.5 1.0 CA A:GLY121 4.7 35.2 1.0 CE A:LYS134 4.7 46.6 1.0 OE1 A:GLU80 5.0 43.8 1.0 CA A:GLU119 5.0 39.3 1.0 O3 A:E4Z903 5.0 48.7 1.0

Manganese binding site 2 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn902 b:69.8 occ:1.00 OD1 A:ASP108 2.0 42.5 1.0 O3 A:E4Z903 2.2 48.7 1.0 O A:HOH1008 2.3 46.0 1.0 O2 A:E4Z903 2.3 41.7 1.0 O A:HOH1001 2.3 34.5 1.0 OE1 A:GLU80 2.4 43.8 1.0 C6 A:E4Z903 3.1 40.3 1.0 CG A:ASP108 3.2 32.6 1.0 C5 A:E4Z903 3.3 34.5 1.0 CD A:GLU80 3.5 49.9 1.0 C4 A:E4Z903 3.6 37.9 1.0 OD2 A:ASP108 3.7 40.8 1.0 MN A:MN901 3.8 50.4 1.0 O A:PRO107 3.9 33.5 1.0 CE1 A:HIS41 4.0 40.9 1.0 N3 A:E4Z903 4.2 45.1 1.0 C A:PRO107 4.3 39.6 1.0 O A:LEU106 4.3 38.4 1.0 CB A:ASP108 4.3 36.0 1.0 OE2 A:GLU80 4.3 60.5 1.0 OE1 A:GLU119 4.4 41.5 1.0 CA A:ASP108 4.4 35.9 1.0 CG A:GLU80 4.4 50.5 1.0 OE2 A:GLU119 4.4 35.4 1.0 N A:ASP108 4.5 33.7 1.0 NE2 A:HIS41 4.5 36.5 1.0 CB A:GLU80 4.5 37.7 1.0 C1 A:E4Z903 4.6 33.8 1.0 C10 A:E4Z903 4.6 42.6 1.0 CD A:GLU119 4.9 36.5 1.0 O1 A:E4Z903 5.0 41.0 1.0

Manganese binding site 3 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn901 b:48.5 occ:1.00 OD2 B:ASP108 2.1 36.9 1.0 O1 B:E4Z903 2.1 45.5 1.0 O B:ILE120 2.2 40.9 1.0 OE2 B:GLU119 2.3 40.2 1.0 O2 B:E4Z903 2.3 40.0 1.0 NE2 B:HIS41 2.4 35.0 1.0 C1 B:E4Z903 2.9 38.7 1.0 C5 B:E4Z903 3.0 39.6 1.0 CG B:ASP108 3.0 39.1 1.0 OD1 B:ASP108 3.1 44.9 1.0 CE1 B:HIS41 3.2 42.8 1.0 CD B:GLU119 3.3 37.2 1.0 C B:ILE120 3.3 35.5 1.0 CD2 B:HIS41 3.4 38.8 1.0 MN B:MN902 3.7 65.0 1.0 N B:ILE120 3.7 38.4 1.0 O B:HOH1001 3.8 39.1 1.0 OE1 B:GLU119 3.9 43.4 1.0 CA B:ILE120 4.0 32.2 1.0 NZ B:LYS134 4.2 62.9 1.0 C2 B:E4Z903 4.2 32.9 1.0 CB B:ILE120 4.2 37.0 1.0 ND1 B:HIS41 4.3 38.1 1.0 C4 B:E4Z903 4.3 37.1 1.0 CG B:GLU119 4.3 42.5 1.0 CB B:ASP108 4.4 44.8 1.0 CG B:HIS41 4.4 35.6 1.0 N B:GLY121 4.4 43.4 1.0 O B:HOH1016 4.5 46.5 1.0 C B:GLU119 4.6 44.6 1.0 CE B:LYS134 4.6 58.9 1.0 CA B:GLY121 4.8 45.0 1.0 OE1 B:GLU80 4.9 44.0 1.0 O3 B:E4Z903 4.9 51.1 1.0 CA B:GLU119 5.0 42.0 1.0

Manganese binding site 4 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn902 b:65.0 occ:1.00 OD1 B:ASP108 2.0 44.9 1.0 O2 B:E4Z903 2.1 40.0 1.0 O3 B:E4Z903 2.2 51.1 1.0 O B:HOH1004 2.3 40.0 1.0 O B:HOH1001 2.4 39.1 1.0 OE1 B:GLU80 2.5 44.0 1.0 CG B:ASP108 3.1 39.1 1.0 C6 B:E4Z903 3.2 41.7 1.0 C5 B:E4Z903 3.2 39.6 1.0 C4 B:E4Z903 3.6 37.1 1.0 CD B:GLU80 3.6 44.4 1.0 MN B:MN901 3.7 48.5 1.0 OD2 B:ASP108 3.7 36.9 1.0 O B:PRO107 3.9 40.5 1.0 CE1 B:HIS41 4.0 42.8 1.0 C B:PRO107 4.2 34.0 1.0 OE1 B:GLU119 4.2 43.4 1.0 CB B:ASP108 4.3 44.8 1.0 N3 B:E4Z903 4.3 46.8 1.0 O B:LEU106 4.3 42.5 1.0 OE2 B:GLU119 4.3 40.2 1.0 CA B:ASP108 4.3 41.1 1.0 N B:ASP108 4.4 38.8 1.0 OE2 B:GLU80 4.4 58.9 1.0 NE2 B:HIS41 4.5 35.0 1.0 CG B:GLU80 4.5 55.1 1.0 C1 B:E4Z903 4.5 38.7 1.0 CB B:GLU80 4.6 42.6 1.0 CD B:GLU119 4.7 37.2 1.0 O1 B:E4Z903 4.8 45.5 1.0 C10 B:E4Z903 4.8 46.5 1.0

Manganese binding site 5 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn901 b:49.8 occ:1.00 O1 C:E4Z903 2.2 38.6 1.0 OD2 C:ASP108 2.2 38.1 1.0 O C:ILE120 2.2 33.9 1.0 OE2 C:GLU119 2.2 39.3 1.0 O2 C:E4Z903 2.4 47.1 1.0 NE2 C:HIS41 2.4 40.4 1.0 C1 C:E4Z903 2.9 35.1 1.0 C5 C:E4Z903 3.0 37.9 1.0 CG C:ASP108 3.0 33.5 1.0 OD1 C:ASP108 3.2 38.5 1.0 CD C:GLU119 3.2 39.0 1.0 CE1 C:HIS41 3.2 33.9 1.0 CD2 C:HIS41 3.3 33.8 1.0 C C:ILE120 3.4 31.8 1.0 OE1 C:GLU119 3.7 36.1 1.0 MN C:MN902 3.7 65.8 1.0 N C:ILE120 3.7 33.4 1.0 O C:HOH1001 3.8 35.3 1.0 CA C:ILE120 4.0 32.7 1.0 NZ C:LYS134 4.2 66.0 1.0 C2 C:E4Z903 4.2 32.5 1.0 ND1 C:HIS41 4.3 36.7 1.0 CB C:ILE120 4.3 43.6 1.0 O C:HOH1027 4.3 38.7 1.0 CG C:GLU119 4.3 37.9 1.0 C4 C:E4Z903 4.4 40.4 1.0 CG C:HIS41 4.4 37.2 1.0 CB C:ASP108 4.4 37.8 1.0 N C:GLY121 4.4 38.7 1.0 C C:GLU119 4.6 39.4 1.0 CE C:LYS134 4.7 54.9 1.0 CA C:GLY121 4.8 37.5 1.0 OE1 C:GLU80 4.8 32.5 1.0 CA C:GLU119 5.0 38.5 1.0 O3 C:E4Z903 5.0 44.7 1.0

Manganese binding site 6 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn902 b:65.8 occ:1.00 O2 C:E4Z903 2.1 47.1 1.0 OD1 C:ASP108 2.1 38.5 1.0 O C:HOH1001 2.2 35.3 1.0 O C:HOH1005 2.2 39.1 1.0 O3 C:E4Z903 2.2 44.7 1.0 OE1 C:GLU80 2.5 32.5 1.0 C6 C:E4Z903 3.1 41.8 1.0 C5 C:E4Z903 3.2 37.9 1.0 CG C:ASP108 3.2 33.5 1.0 CD C:GLU80 3.6 39.0 1.0 C4 C:E4Z903 3.6 40.4 1.0 MN C:MN901 3.7 49.8 1.0 OD2 C:ASP108 3.8 38.1 1.0 O C:PRO107 3.9 36.0 1.0 CE1 C:HIS41 4.0 33.9 1.0 OE1 C:GLU119 4.2 36.1 1.0 C C:PRO107 4.2 36.7 1.0 N3 C:E4Z903 4.3 44.7 1.0 O C:LEU106 4.3 37.0 1.0 OE2 C:GLU80 4.4 52.9 1.0 CB C:ASP108 4.4 37.8 1.0 CA C:ASP108 4.4 38.4 1.0 N C:ASP108 4.5 35.0 1.0 NE2 C:HIS41 4.5 40.4 1.0 OE2 C:GLU119 4.5 39.3 1.0 C1 C:E4Z903 4.5 35.1 1.0 CG C:GLU80 4.5 47.7 1.0 CB C:GLU80 4.6 46.1 1.0 C10 C:E4Z903 4.8 40.6 1.0 CD C:GLU119 4.8 39.0 1.0 O1 C:E4Z903 4.8 38.6 1.0

Manganese binding site 7 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn901 b:49.6 occ:1.00 OD2 D:ASP108 2.1 42.5 1.0 O1 D:E4Z903 2.2 44.0 1.0 O D:ILE120 2.2 41.7 1.0 OE2 D:GLU119 2.3 39.4 1.0 NE2 D:HIS41 2.3 43.2 1.0 O2 D:E4Z903 2.3 44.7 1.0 C1 D:E4Z903 2.9 44.1 1.0 C5 D:E4Z903 3.0 42.3 1.0 CG D:ASP108 3.0 41.8 1.0 CE1 D:HIS41 3.2 42.5 1.0 OD1 D:ASP108 3.2 45.3 1.0 CD2 D:HIS41 3.3 38.4 1.0 C D:ILE120 3.3 37.6 1.0 CD D:GLU119 3.3 38.7 1.0 MN D:MN902 3.6 70.8 1.0 N D:ILE120 3.8 36.3 1.0 OE1 D:GLU119 3.9 45.0 1.0 O D:HOH1003 3.9 45.3 1.0 CA D:ILE120 4.0 34.5 1.0 NZ D:LYS134 4.1 60.8 1.0 C2 D:E4Z903 4.2 38.6 1.0 ND1 D:HIS41 4.2 38.8 1.0 CB D:ILE120 4.3 44.3 1.0 C4 D:E4Z903 4.3 43.9 1.0 O D:HOH1027 4.3 47.9 1.0 CG D:HIS41 4.4 40.8 1.0 CG D:GLU119 4.4 44.5 1.0 N D:GLY121 4.4 38.3 1.0 CB D:ASP108 4.4 41.1 1.0 CE D:LYS134 4.6 52.4 1.0 C D:GLU119 4.7 41.6 1.0 CA D:GLY121 4.7 39.4 1.0 OE1 D:GLU80 4.8 45.5 1.0 O3 D:E4Z903 4.9 57.8 1.0

Manganese binding site 8 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn902 b:70.8 occ:1.00 OD1 D:ASP108 2.0 45.3 1.0 O2 D:E4Z903 2.1 44.7 1.0 O D:HOH1003 2.2 45.3 1.0 O3 D:E4Z903 2.3 57.8 1.0 OE1 D:GLU80 2.4 45.5 1.0 O D:HOH1007 2.4 36.7 1.0 CG D:ASP108 3.1 41.8 1.0 C5 D:E4Z903 3.1 42.3 1.0 C6 D:E4Z903 3.1 51.6 1.0 CD D:GLU80 3.5 54.3 1.0 OD2 D:ASP108 3.6 42.5 1.0 C4 D:E4Z903 3.6 43.9 1.0 MN D:MN901 3.6 49.6 1.0 CE1 D:HIS41 3.9 42.5 1.0 O D:PRO107 4.0 39.8 1.0 OE2 D:GLU119 4.2 39.4 1.0 N3 D:E4Z903 4.3 47.7 1.0 CB D:ASP108 4.3 41.1 1.0 C D:PRO107 4.3 40.7 1.0 OE1 D:GLU119 4.3 45.0 1.0 OE2 D:GLU80 4.3 51.9 1.0 O D:LEU106 4.4 40.4 1.0 CA D:ASP108 4.4 41.2 1.0 NE2 D:HIS41 4.4 43.2 1.0 CG D:GLU80 4.4 45.6 1.0 C1 D:E4Z903 4.4 44.1 1.0 N D:ASP108 4.5 40.6 1.0 CB D:GLU80 4.6 44.0 1.0 CD D:GLU119 4.7 38.7 1.0 O1 D:E4Z903 4.7 44.0 1.0 C10 D:E4Z903 4.8 44.2 1.0 O D:HOH1035 4.9 54.2 1.0 N1 D:E4Z903 5.0 45.1 1.0

Manganese binding site 9 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn901 b:48.6 occ:1.00 O1 E:E4Z903 2.1 43.5 1.0 O E:ILE120 2.2 34.7 1.0 OE2 E:GLU119 2.2 40.6 1.0 OD2 E:ASP108 2.2 43.4 1.0 O2 E:E4Z903 2.3 41.6 1.0 NE2 E:HIS41 2.4 32.8 1.0 C1 E:E4Z903 2.9 44.2 1.0 C5 E:E4Z903 2.9 38.7 1.0 CG E:ASP108 3.1 39.1 1.0 CE1 E:HIS41 3.2 40.1 1.0 CD E:GLU119 3.2 33.2 1.0 OD1 E:ASP108 3.2 46.5 1.0 CD2 E:HIS41 3.3 38.6 1.0 C E:ILE120 3.3 35.1 1.0 MN E:MN902 3.7 71.5 1.0 N E:ILE120 3.7 42.8 1.0 OE1 E:GLU119 3.7 42.2 1.0 O E:HOH1001 3.9 50.0 1.0 CA E:ILE120 4.0 35.7 1.0 NZ E:LYS134 4.1 56.9 1.0 C2 E:E4Z903 4.2 35.6 1.0 CB E:ILE120 4.3 46.7 1.0 C4 E:E4Z903 4.3 38.4 1.0 ND1 E:HIS41 4.3 46.3 1.0 CG E:GLU119 4.4 41.8 1.0 CG E:HIS41 4.4 36.6 1.0 O E:HOH1019 4.4 43.0 1.0 N E:GLY121 4.4 40.3 1.0 CB E:ASP108 4.5 43.7 1.0 CE E:LYS134 4.5 52.3 1.0 C E:GLU119 4.7 45.9 1.0 CA E:GLY121 4.8 41.9 1.0 OE1 E:GLU80 4.8 45.4 1.0 O3 E:E4Z903 4.8 52.2 1.0

Manganese binding site 10 out of 12 in the Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Influenza A/California/04/2009 (PH1N1) Endonuclease with Bound Inhibitor, Baloxavir Acid (Bxa) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn902 b:71.5 occ:1.00 O3 E:E4Z903 2.1 52.2 1.0 OD1 E:ASP108 2.1 46.5 1.0 O2 E:E4Z903 2.1 41.6 1.0 O E:HOH1011 2.2 43.6 1.0 O E:HOH1001 2.4 50.0 1.0 OE1 E:GLU80 2.5 45.4 1.0 C6 E:E4Z903 3.1 42.9 1.0 C5 E:E4Z903 3.2 38.7 1.0 CG E:ASP108 3.2 39.1 1.0 C4 E:E4Z903 3.6 38.4 1.0 CD E:GLU80 3.6 56.5 1.0 OD2 E:ASP108 3.7 43.4 1.0 MN E:MN901 3.7 48.6 1.0 O E:PRO107 3.9 40.3 1.0 CE1 E:HIS41 4.1 40.1 1.0 OE1 E:GLU119 4.1 42.2 1.0 N3 E:E4Z903 4.2 43.0 1.0 C E:PRO107 4.2 40.7 1.0 O E:LEU106 4.3 43.2 1.0 OE2 E:GLU80 4.3 52.6 1.0 OE2 E:GLU119 4.4 40.6 1.0 CB E:ASP108 4.4 43.7 1.0 CA E:ASP108 4.4 43.5 1.0 N E:ASP108 4.5 40.7 1.0 CG E:GLU80 4.5 55.2 1.0 C1 E:E4Z903 4.5 44.2 1.0 NE2 E:HIS41 4.5 32.8 1.0 O E:HOH1013 4.6 46.5 1.0 CB E:GLU80 4.6 45.1 1.0 CD E:GLU119 4.7 33.2 1.0 C10 E:E4Z903 4.7 41.4 1.0 O1 E:E4Z903 4.8 43.5 1.0 N1 E:E4Z903 5.0 37.4 1.0

S.Omoto, V.Speranzini, T.Hashimoto, T.Noshi, H.Yamaguchi, M.Kawai, K.Kawaguchi, T.Uehara, T.Shishido, A.Naito, S.Cusack. Characterization of Influenza Virus Variants Induced By Treatment with the Endonuclease Inhibitor Baloxavir Marboxil. Sci Rep V. 8 9633 2018.
ISSN: ESSN 2045-2322
PubMed: 29941893
DOI: 10.1038/S41598-018-27890-4