Manganese in PDB 4mk2: 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease

The structure of 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk2 was solved by J.D.Bauman, D.Patel, K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.24 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.694, 101.432, 66.120, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.7

The binding sites of Manganese atom in the 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease (pdb code 4mk2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk2:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:25.3 occ:1.00 OE2 A:GLU119 2.1 24.9 1.0 OD2 A:ASP108 2.1 21.9 1.0 O A:ILE120 2.2 23.8 1.0 O01 A:28B306 2.2 23.0 1.0 O04 A:28B306 2.2 24.4 1.0 NE2 A:HIS41 2.3 21.4 1.0 C02 A:28B306 2.9 25.3 1.0 C03 A:28B306 2.9 28.4 1.0 CG A:ASP108 3.1 20.0 1.0 CE1 A:HIS41 3.1 24.0 1.0 CD A:GLU119 3.2 28.4 1.0 HE1 A:HIS41 3.2 28.8 1.0 CD2 A:HIS41 3.3 19.8 1.0 H A:ILE120 3.3 27.0 1.0 C A:ILE120 3.3 24.1 1.0 OD1 A:ASP108 3.3 20.3 1.0 HD2 A:HIS41 3.5 23.8 1.0 HZ1 A:LYS134 3.5 39.0 1.0 HB A:ILE120 3.6 28.8 1.0 N A:ILE120 3.7 22.5 1.0 HZ2 A:LYS134 3.8 39.0 1.0 OE1 A:GLU119 3.8 25.1 1.0 MN A:MN302 3.8 46.0 1.0 HE3 A:LYS134 3.8 41.4 1.0 O A:HOH500 3.9 24.6 1.0 CA A:ILE120 4.0 21.1 1.0 HG3 A:GLU119 4.0 27.5 1.0 HA2 A:GLY121 4.0 27.8 1.0 NZ A:LYS134 4.0 32.5 1.0 O A:HOH510 4.1 36.3 1.0 ND1 A:HIS41 4.2 20.8 1.0 N16 A:28B306 4.2 29.1 1.0 CG A:GLU119 4.2 22.9 1.0 O A:HOH403 4.2 26.3 1.0 CB A:ILE120 4.2 24.0 1.0 C05 A:28B306 4.3 28.1 1.0 CG A:HIS41 4.3 23.0 1.0 N A:GLY121 4.4 23.1 1.0 CB A:ASP108 4.4 20.9 1.0 CE A:LYS134 4.5 34.5 1.0 HA A:GLU119 4.5 26.4 1.0 HG22 A:ILE120 4.5 29.7 1.0 HB2 A:ASP108 4.6 25.0 1.0 C A:GLU119 4.6 24.4 1.0 CA A:GLY121 4.7 23.1 1.0 OE2 A:GLU80 4.7 23.8 1.0 HZ3 A:LYS134 4.8 39.0 1.0 HB3 A:ASP108 4.8 25.0 1.0 HG2 A:GLU119 4.8 27.5 1.0 HA A:ILE120 4.9 25.3 1.0 HD1 A:HIS41 4.9 25.0 1.0 HE2 A:LYS134 5.0 41.4 1.0 CA A:GLU119 5.0 22.0 1.0 CG2 A:ILE120 5.0 24.7 1.0

Manganese binding site 2 out of 3 in the 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:46.0 occ:1.00 OE2 A:GLU80 2.1 23.8 1.0 OD1 A:ASP108 2.1 20.3 1.0 O A:HOH500 2.2 24.6 1.0 O A:HOH430 2.2 22.7 1.0 O A:HOH423 2.2 22.1 1.0 O01 A:28B306 2.2 23.0 1.0 C02 A:28B306 3.1 25.3 1.0 HE1 A:HIS41 3.1 28.8 1.0 CD A:GLU80 3.2 23.4 1.0 CG A:ASP108 3.2 20.0 1.0 N16 A:28B306 3.3 29.1 1.0 HB2 A:GLU80 3.4 29.9 1.0 O A:HOH574 3.6 62.1 1.0 OD2 A:ASP108 3.7 21.9 1.0 HA A:ASP108 3.7 22.3 1.0 MN A:MN303 3.8 0.0 1.0 MN A:MN301 3.8 25.3 1.0 CE1 A:HIS41 3.9 24.0 1.0 OE1 A:GLU80 3.9 26.9 1.0 CG A:GLU80 4.0 23.4 1.0 HG2 A:GLU80 4.0 28.1 1.0 CB A:GLU80 4.1 24.9 1.0 O A:HOH510 4.1 36.3 1.0 O A:PRO107 4.2 24.5 1.0 O A:LEU106 4.3 26.8 1.0 O A:HOH494 4.3 42.0 1.0 HA A:GLU80 4.3 27.5 1.0 CB A:ASP108 4.3 20.9 1.0 CA A:ASP108 4.3 18.6 1.0 C A:PRO107 4.4 22.2 1.0 OE1 A:GLU119 4.4 25.1 1.0 C03 A:28B306 4.4 28.4 1.0 NE2 A:HIS41 4.4 21.4 1.0 N A:ASP108 4.5 21.1 1.0 OE2 A:GLU119 4.5 24.9 1.0 C15 A:28B306 4.7 29.4 1.0 CA A:GLU80 4.7 22.9 1.0 HB3 A:ASP108 4.8 25.0 1.0 HA A:PRO107 4.9 29.9 1.0 HB3 A:GLU80 4.9 29.9 1.0 CD A:GLU119 4.9 28.4 1.0 O04 A:28B306 4.9 24.4 1.0 HG3 A:GLU80 4.9 28.1 1.0 H A:ASP108 4.9 25.3 1.0 ND1 A:HIS41 4.9 20.8 1.0

Manganese binding site 3 out of 3 in the 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 3-(5-Hydroxy-6-Oxo-1,6-Dihydropyridin-3-Yl)Benzonitrile Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:0.0 occ:1.00 O A:HOH574 2.2 62.1 1.0 OH A:TYR24 2.3 76.0 1.0 OE1 A:GLU80 2.4 26.9 1.0 O A:HOH430 2.4 22.7 1.0 HH A:TYR24 2.6 91.2 1.0 OE2 A:GLU80 2.9 23.8 1.0 CD A:GLU80 3.0 23.4 1.0 CZ A:TYR24 3.6 77.7 1.0 N16 A:28B306 3.6 29.1 1.0 O A:HOH513 3.6 32.9 1.0 O A:HOH594 3.6 57.8 1.0 HE2 A:TYR24 3.7 95.0 1.0 MN A:MN302 3.8 46.0 1.0 O A:HOH423 3.9 22.1 1.0 O A:HOH585 3.9 57.4 1.0 CE2 A:TYR24 4.1 79.2 1.0 C15 A:28B306 4.1 29.4 1.0 HA A:GLU80 4.4 27.5 1.0 H A:GLY81 4.5 30.7 1.0 CG A:GLU80 4.5 23.4 1.0 C02 A:28B306 4.7 25.3 1.0 CE1 A:TYR24 4.7 75.2 1.0 HG3 A:GLU80 4.8 28.1 1.0 HE1 A:TYR24 4.8 90.3 1.0 O01 A:28B306 4.8 23.0 1.0 HB1 A:ALA20 4.9 39.9 1.0 O A:HOH555 4.9 51.1 1.0 HG2 A:GLU80 5.0 28.1 1.0

J.D.Bauman, D.Patel, S.F.Baker, R.S.Vijayan, A.Xiang, A.K.Parhi, L.Martinez-Sobrido, E.J.Lavoie, K.Das, E.Arnold. Crystallographic Fragment Screening and Structure-Based Optimization Yields A New Class of Influenza Endonuclease Inhibitors. Acs Chem.Biol. V. 8 2501 2013.
ISSN: ISSN 1554-8929
PubMed: 23978130
DOI: 10.1021/CB400400J