Manganese in PDB 4e5j: Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5

The structure of Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5, PDB code: 4e5j was solved by R.M.Dubois, P.J.Slavish, T.R.Webb, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	126.098, 134.087, 126.640, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 29

The binding sites of Manganese atom in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5 (pdb code 4e5j). 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 Pan Bound to Compound 5, PDB code: 4e5j:
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 Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn305 b:26.5 occ:1.00 O2 A:581303 2.0 27.0 1.0 OE2 A:GLU119 2.1 27.6 1.0 OD2 A:ASP108 2.2 26.1 1.0 O A:ILE120 2.2 27.4 1.0 O1 A:581303 2.2 33.6 1.0 NE2 A:HIS41 2.3 23.5 1.0 C9 A:581303 2.8 32.5 1.0 C10 A:581303 2.9 33.6 1.0 CG A:ASP108 3.0 29.8 1.0 CE1 A:HIS41 3.0 23.5 1.0 OD1 A:ASP108 3.1 27.5 1.0 CD A:GLU119 3.2 30.5 1.0 CD2 A:HIS41 3.3 24.2 1.0 C A:ILE120 3.4 28.2 1.0 MN A:MN306 3.7 49.5 1.0 N A:ILE120 3.8 28.6 1.0 OE1 A:GLU119 3.8 33.6 1.0 CA A:ILE120 4.1 28.3 1.0 ND1 A:HIS41 4.1 22.5 1.0 N2 A:581303 4.2 35.4 1.0 CG A:GLU119 4.2 30.2 1.0 C8 A:581303 4.2 35.1 1.0 CG A:HIS41 4.3 24.4 1.0 NZ A:LYS134 4.3 49.6 1.0 CB A:ASP108 4.4 31.0 1.0 O A:HOH401 4.4 23.4 1.0 CB A:ILE120 4.4 28.2 1.0 N A:GLY121 4.5 27.5 1.0 OE1 A:GLU80 4.6 35.2 1.0 CA A:GLY121 4.7 27.4 1.0 C A:GLU119 4.7 28.9 1.0 O3 A:581303 4.9 35.3 1.0 CE A:LYS134 4.9 48.3 1.0 CA A:GLU119 5.0 29.4 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn306 b:49.5 occ:1.00 O3 A:581303 2.0 35.3 1.0 OD1 A:ASP108 2.0 27.5 1.0 OE1 A:GLU80 2.1 35.2 1.0 O2 A:581303 2.2 27.0 1.0 C11 A:581303 3.0 37.1 1.0 CG A:ASP108 3.1 29.8 1.0 C9 A:581303 3.2 32.5 1.0 CD A:GLU80 3.2 36.8 1.0 C8 A:581303 3.5 35.1 1.0 O A:HOH411 3.6 30.0 1.0 MN A:MN305 3.7 26.5 1.0 OD2 A:ASP108 3.7 26.1 1.0 CE1 A:HIS41 3.9 23.5 1.0 OE2 A:GLU80 4.1 37.0 1.0 CG A:GLU80 4.1 37.1 1.0 O A:LEU106 4.1 37.3 1.0 O4 A:581303 4.1 39.9 1.0 O A:PRO107 4.2 33.7 1.0 CB A:ASP108 4.3 31.0 1.0 CB A:GLU80 4.3 37.6 1.0 OE2 A:GLU119 4.3 27.6 1.0 C A:PRO107 4.4 33.5 1.0 CA A:ASP108 4.4 31.8 1.0 OE1 A:GLU119 4.4 33.6 1.0 NE2 A:HIS41 4.4 23.5 1.0 N A:ASP108 4.5 32.4 1.0 C10 A:581303 4.5 33.6 1.0 CD A:GLU119 4.8 30.5 1.0 N1 A:581303 4.8 38.3 1.0 ND1 A:HIS41 4.9 22.5 1.0 O1 A:581303 5.0 33.6 1.0 C A:LEU106 5.0 37.2 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn305 b:30.1 occ:1.00 O2 B:581303 2.0 40.0 1.0 OD2 B:ASP108 2.1 30.7 1.0 O B:ILE120 2.1 29.9 1.0 OE1 B:GLU119 2.2 34.6 1.0 O1 B:581303 2.2 40.6 1.0 NE2 B:HIS41 2.3 27.2 1.0 C9 B:581303 2.8 41.7 1.0 C10 B:581303 2.8 43.0 1.0 CG B:ASP108 3.1 31.2 1.0 CE1 B:HIS41 3.2 25.9 1.0 C B:ILE120 3.3 30.2 1.0 CD B:GLU119 3.3 34.0 1.0 OD1 B:ASP108 3.3 28.3 1.0 CD2 B:HIS41 3.3 27.8 1.0 N B:ILE120 3.7 30.1 1.0 NZ B:LYS134 3.8 52.9 1.0 MN B:MN306 3.8 55.1 1.0 OE2 B:GLU119 3.9 35.4 1.0 CA B:ILE120 4.0 30.0 1.0 N2 B:581303 4.1 44.6 1.0 C8 B:581303 4.2 43.1 1.0 ND1 B:HIS41 4.3 28.1 1.0 CG B:GLU119 4.3 32.2 1.0 N B:GLY121 4.4 29.9 1.0 O B:HOH401 4.4 29.2 1.0 CG B:HIS41 4.4 28.6 1.0 CB B:ASP108 4.5 32.6 1.0 CB B:ILE120 4.5 30.6 1.0 CA B:GLY121 4.6 29.6 1.0 OE1 B:GLU80 4.7 38.6 1.0 C B:GLU119 4.7 30.5 1.0 O3 B:581303 4.7 45.1 1.0 CE B:LYS134 5.0 53.6 1.0 C11 B:581303 5.0 43.7 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn306 b:55.1 occ:1.00 O3 B:581303 1.8 45.1 1.0 OD1 B:ASP108 2.2 28.3 1.0 OE1 B:GLU80 2.2 38.6 1.0 O2 B:581303 2.2 40.0 1.0 C11 B:581303 2.9 43.7 1.0 C9 B:581303 3.2 41.7 1.0 CG B:ASP108 3.2 31.2 1.0 CD B:GLU80 3.3 38.4 1.0 C8 B:581303 3.4 43.1 1.0 OD2 B:ASP108 3.7 30.7 1.0 MN B:MN305 3.8 30.1 1.0 O4 B:581303 3.9 43.4 1.0 CE1 B:HIS41 4.0 25.9 1.0 O B:PRO107 4.0 32.9 1.0 O B:LEU106 4.0 38.6 1.0 OE2 B:GLU80 4.1 37.9 1.0 CG B:GLU80 4.1 37.6 1.0 C B:PRO107 4.3 34.2 1.0 CB B:GLU80 4.3 37.8 1.0 CB B:ASP108 4.4 32.6 1.0 OE1 B:GLU119 4.4 34.6 1.0 CA B:ASP108 4.4 33.1 1.0 OE2 B:GLU119 4.4 35.4 1.0 NE2 B:HIS41 4.5 27.2 1.0 N B:ASP108 4.5 33.4 1.0 C10 B:581303 4.6 43.0 1.0 N1 B:581303 4.8 45.5 1.0 CD B:GLU119 4.9 34.0 1.0 C B:LEU106 5.0 38.3 1.0 O1 B:581303 5.0 40.6 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn305 b:31.5 occ:1.00 O1 C:581303 2.1 41.3 1.0 O C:ILE120 2.1 30.5 1.0 OD2 C:ASP108 2.2 31.8 1.0 O2 C:581303 2.2 41.3 1.0 NE2 C:HIS41 2.2 22.7 1.0 OE1 C:GLU119 2.3 34.6 1.0 C10 C:581303 2.8 42.5 1.0 C9 C:581303 2.9 42.4 1.0 CE1 C:HIS41 3.0 21.5 1.0 CG C:ASP108 3.0 35.2 1.0 OD1 C:ASP108 3.1 32.7 1.0 C C:ILE120 3.3 30.3 1.0 CD2 C:HIS41 3.3 24.2 1.0 CD C:GLU119 3.4 35.9 1.0 N C:ILE120 3.7 31.9 1.0 MN C:MN306 3.8 52.0 1.0 NZ C:LYS134 3.9 60.1 1.0 CA C:ILE120 4.0 30.9 1.0 OE2 C:GLU119 4.0 38.9 1.0 N2 C:581303 4.1 43.9 1.0 ND1 C:HIS41 4.1 21.8 1.0 CG C:HIS41 4.3 23.5 1.0 C8 C:581303 4.3 44.0 1.0 N C:GLY121 4.4 29.5 1.0 O C:HOH401 4.4 30.9 1.0 CG C:GLU119 4.4 34.3 1.0 CB C:ASP108 4.4 35.9 1.0 CB C:ILE120 4.4 31.1 1.0 OE1 C:GLU80 4.6 37.1 1.0 CA C:GLY121 4.6 28.4 1.0 C C:GLU119 4.8 33.0 1.0 O4 C:581303 5.0 43.3 1.0 CG2 C:ILE120 5.0 30.5 1.0 CE C:LYS134 5.0 59.0 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn306 b:52.0 occ:1.00 O2 C:581303 2.0 41.3 1.0 O4 C:581303 2.1 43.3 1.0 OE1 C:GLU80 2.1 37.1 1.0 OD1 C:ASP108 2.2 32.7 1.0 C11 C:581303 3.0 44.8 1.0 C9 C:581303 3.1 42.4 1.0 CD C:GLU80 3.2 37.2 1.0 CG C:ASP108 3.3 35.2 1.0 C8 C:581303 3.5 44.0 1.0 MN C:MN305 3.8 31.5 1.0 CE1 C:HIS41 3.9 21.5 1.0 OD2 C:ASP108 3.9 31.8 1.0 OE2 C:GLU80 3.9 36.9 1.0 O3 C:581303 4.1 47.5 1.0 CG C:GLU80 4.1 37.0 1.0 O C:HOH411 4.1 30.0 1.0 O C:PRO107 4.1 36.8 1.0 O C:LEU106 4.1 41.1 1.0 CB C:GLU80 4.2 36.8 1.0 C C:PRO107 4.4 37.4 1.0 CA C:ASP108 4.4 36.3 1.0 CB C:ASP108 4.4 35.9 1.0 C10 C:581303 4.4 42.5 1.0 OE1 C:GLU119 4.5 34.6 1.0 NE2 C:HIS41 4.5 22.7 1.0 N C:ASP108 4.6 36.6 1.0 OE2 C:GLU119 4.6 38.9 1.0 O1 C:581303 4.8 41.3 1.0 N1 C:581303 4.8 45.5 1.0 ND1 C:HIS41 4.9 21.8 1.0 CA C:GLU80 4.9 37.2 1.0 CD C:GLU119 5.0 35.9 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn305 b:30.4 occ:1.00 OD2 D:ASP108 2.1 33.8 1.0 O2 D:581303 2.2 38.5 1.0 O D:ILE120 2.2 30.1 1.0 O1 D:581303 2.2 40.5 1.0 NE2 D:HIS41 2.2 27.6 1.0 OE1 D:GLU119 2.3 26.7 1.0 C9 D:581303 2.9 42.5 1.0 C10 D:581303 2.9 43.3 1.0 CG D:ASP108 3.0 34.3 1.0 CE1 D:HIS41 3.1 27.1 1.0 OD1 D:ASP108 3.2 32.9 1.0 CD D:GLU119 3.3 29.8 1.0 CD2 D:HIS41 3.3 28.8 1.0 C D:ILE120 3.3 30.2 1.0 N D:ILE120 3.7 30.5 1.0 MN D:MN306 3.8 56.0 1.0 OE2 D:GLU119 3.8 32.7 1.0 NZ D:LYS134 3.8 54.1 1.0 CA D:ILE120 4.0 29.8 1.0 ND1 D:HIS41 4.2 28.5 1.0 N2 D:581303 4.2 44.9 1.0 C8 D:581303 4.3 44.6 1.0 O D:HOH401 4.3 30.6 1.0 CB D:ASP108 4.3 35.9 1.0 CG D:GLU119 4.3 30.9 1.0 CG D:HIS41 4.3 29.1 1.0 CB D:ILE120 4.4 30.5 1.0 N D:GLY121 4.4 30.5 1.0 CA D:GLY121 4.7 29.0 1.0 OE1 D:GLU80 4.7 42.8 1.0 C D:GLU119 4.7 31.0 1.0 CE D:LYS134 4.8 53.4 1.0 O4 D:581303 5.0 45.6 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of Avian Influenza Virus Pan Bound to Compound 5


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 Pan Bound to Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn306 b:56.0 occ:1.00 O4 D:581303 2.1 45.6 1.0 O2 D:581303 2.1 38.5 1.0 OD1 D:ASP108 2.2 32.9 1.0 OE1 D:GLU80 2.3 42.8 1.0 C11 D:581303 3.0 45.5 1.0 C9 D:581303 3.2 42.5 1.0 CG D:ASP108 3.2 34.3 1.0 CD D:GLU80 3.2 42.2 1.0 C8 D:581303 3.5 44.6 1.0 MN D:MN305 3.8 30.4 1.0 OD2 D:ASP108 3.8 33.8 1.0 O D:HOH414 3.8 30.0 1.0 CE1 D:HIS41 3.8 27.1 1.0 OE2 D:GLU80 4.0 41.7 1.0 CG D:GLU80 4.1 42.2 1.0 O3 D:581303 4.1 46.8 1.0 O D:PRO107 4.2 37.0 1.0 CB D:GLU80 4.2 41.5 1.0 O D:LEU106 4.2 41.2 1.0 CB D:ASP108 4.4 35.9 1.0 CA D:ASP108 4.4 36.1 1.0 C D:PRO107 4.4 37.6 1.0 NE2 D:HIS41 4.4 27.6 1.0 OE2 D:GLU119 4.5 32.7 1.0 C10 D:581303 4.5 43.3 1.0 N D:ASP108 4.6 36.4 1.0 OE1 D:GLU119 4.6 26.7 1.0 N1 D:581303 4.8 46.0 1.0 ND1 D:HIS41 4.9 28.5 1.0 CA D:GLU80 4.9 41.5 1.0 O1 D:581303 5.0 40.5 1.0 CD D:GLU119 5.0 29.8 1.0

R.M.Dubois, P.J.Slavish, B.M.Baughman, M.K.Yun, J.Bao, R.J.Webby, T.R.Webb, S.W.White. Structural and Biochemical Basis For Development of Influenza Virus Inhibitors Targeting the Pa Endonuclease. Plos Pathog. V. 8 02830 2012.
ISSN: ISSN 1553-7366
PubMed: 22876176
DOI: 10.1371/JOURNAL.PPAT.1002830