Manganese in PDB 4mk5: 6-(3-Methoxyphenyl)Pyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease

The structure of 6-(3-Methoxyphenyl)Pyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk5 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)	33.10 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.195, 101.683, 66.206, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.2

The binding sites of Manganese atom in the 6-(3-Methoxyphenyl)Pyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease (pdb code 4mk5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the 6-(3-Methoxyphenyl)Pyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk5:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the 6-(3-Methoxyphenyl)Pyridine-2,3-Diol 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 6-(3-Methoxyphenyl)Pyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:22.0 occ:1.00 OE2 A:GLU119 2.1 23.3 1.0 O A:ILE120 2.1 20.4 1.0 OD2 A:ASP108 2.2 20.1 1.0 O01 A:28A306 2.2 20.2 1.0 O16 A:28A306 2.2 19.9 1.0 NE2 A:HIS41 2.2 18.6 1.0 C15 A:28A306 2.9 21.2 1.0 C02 A:28A306 2.9 21.1 1.0 CE1 A:HIS41 3.0 18.4 1.0 HE1 A:HIS41 3.1 22.1 1.0 CG A:ASP108 3.1 19.5 1.0 CD A:GLU119 3.2 23.2 1.0 C A:ILE120 3.3 20.4 1.0 CD2 A:HIS41 3.3 18.9 1.0 OD1 A:ASP108 3.4 19.1 1.0 H A:ILE120 3.4 24.8 1.0 HE3 A:LYS134 3.4 42.0 1.0 HD2 A:HIS41 3.6 22.6 1.0 HZ1 A:LYS134 3.6 36.7 1.0 HB A:ILE120 3.6 27.4 1.0 N A:ILE120 3.8 20.7 1.0 OE1 A:GLU119 3.8 24.0 1.0 MN A:MN302 3.8 23.4 0.8 HZ3 A:LYS134 3.9 36.7 1.0 HA2 A:GLY121 3.9 25.8 1.0 CA A:ILE120 4.0 20.1 1.0 O A:HOH491 4.0 24.6 1.0 HG3 A:GLU119 4.0 27.7 1.0 NZ A:LYS134 4.0 30.6 1.0 ND1 A:HIS41 4.1 18.7 1.0 O A:HOH499 4.2 33.9 1.0 N14 A:28A306 4.2 22.6 1.0 CE A:LYS134 4.2 35.0 1.0 CG A:GLU119 4.2 23.1 1.0 CB A:ILE120 4.2 22.8 1.0 C03 A:28A306 4.3 21.6 1.0 CG A:HIS41 4.3 19.0 1.0 N A:GLY121 4.4 21.5 1.0 O A:HOH404 4.4 21.9 1.0 CB A:ASP108 4.5 20.1 1.0 HA A:GLU119 4.5 25.9 1.0 HG22 A:ILE120 4.5 26.1 1.0 HB2 A:ASP108 4.6 24.1 1.0 C A:GLU119 4.6 21.9 1.0 CA A:GLY121 4.6 21.5 1.0 OE2 A:GLU80 4.7 21.2 1.0 HD3 A:LYS134 4.8 48.5 1.0 HB3 A:ASP108 4.8 24.1 1.0 HG2 A:GLU119 4.9 27.7 1.0 HD1 A:HIS41 4.9 22.4 1.0 HA A:ILE120 4.9 24.2 1.0 HZ2 A:LYS134 4.9 36.7 1.0 HE2 A:LYS134 4.9 42.0 1.0 CA A:GLU119 5.0 21.6 1.0 CG2 A:ILE120 5.0 21.7 1.0 CD A:LYS134 5.0 40.5 1.0

Manganese binding site 2 out of 3 in the 6-(3-Methoxyphenyl)Pyridine-2,3-Diol 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 6-(3-Methoxyphenyl)Pyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:23.4 occ:0.81 OE2 A:GLU80 2.1 21.2 1.0 O16 A:28A306 2.2 19.9 1.0 OD1 A:ASP108 2.2 19.1 1.0 O A:HOH491 2.2 24.6 1.0 O A:HOH426 2.2 20.4 1.0 O A:HOH432 2.2 23.8 1.0 HE1 A:HIS41 3.1 22.1 1.0 C15 A:28A306 3.2 21.2 1.0 CD A:GLU80 3.2 21.0 1.0 CG A:ASP108 3.2 19.5 1.0 N14 A:28A306 3.3 22.6 1.0 HB2 A:GLU80 3.5 26.9 1.0 OD2 A:ASP108 3.7 20.1 1.0 HA A:ASP108 3.8 25.8 1.0 MN A:MN301 3.8 22.0 1.0 CE1 A:HIS41 3.9 18.4 1.0 OE1 A:GLU80 4.0 22.4 1.0 O A:HOH515 4.0 40.2 1.0 CG A:GLU80 4.1 20.6 1.0 HG2 A:GLU80 4.1 24.7 1.0 MN A:MN303 4.1 42.4 0.4 O A:PRO107 4.2 24.3 1.0 CB A:GLU80 4.2 22.4 1.0 O A:LEU106 4.3 24.9 1.0 O A:HOH499 4.3 33.9 1.0 HA A:GLU80 4.4 27.7 1.0 CB A:ASP108 4.4 20.1 1.0 OE1 A:GLU119 4.4 24.0 1.0 C A:PRO107 4.4 24.3 1.0 OE2 A:GLU119 4.4 23.3 1.0 CA A:ASP108 4.4 21.5 1.0 C02 A:28A306 4.4 21.1 1.0 NE2 A:HIS41 4.5 18.6 1.0 N A:ASP108 4.6 23.2 1.0 C05 A:28A306 4.6 23.4 1.0 CA A:GLU80 4.8 23.1 1.0 HB3 A:ASP108 4.8 24.1 1.0 CD A:GLU119 4.9 23.2 1.0 O01 A:28A306 4.9 20.2 1.0 HA A:PRO107 4.9 31.0 1.0 ND1 A:HIS41 4.9 18.7 1.0 HG3 A:GLU80 5.0 24.7 1.0

Manganese binding site 3 out of 3 in the 6-(3-Methoxyphenyl)Pyridine-2,3-Diol 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 6-(3-Methoxyphenyl)Pyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:42.4 occ:0.42 O A:HOH515 2.0 40.2 1.0 OE1 A:GLU80 2.3 22.4 1.0 CD A:GLU80 3.1 21.0 1.0 O A:HOH432 3.2 23.8 1.0 OE2 A:GLU80 3.2 21.2 1.0 O A:HOH536 3.4 59.0 1.0 O A:HOH504 3.4 36.8 1.0 C13 A:28A306 3.5 30.1 1.0 C12 A:28A306 3.5 31.6 1.0 O A:HOH415 3.6 43.6 1.0 O A:HOH409 3.6 46.1 1.0 O A:HOH426 3.7 20.4 1.0 H A:GLY81 3.8 31.1 1.0 HA A:GLU80 3.8 27.7 1.0 MN A:MN302 4.1 23.4 0.8 HE2 A:TYR24 4.2 55.3 1.0 O A:HOH500 4.4 34.9 1.0 CG A:GLU80 4.5 20.6 1.0 C06 A:28A306 4.5 26.3 1.0 N14 A:28A306 4.6 22.6 1.0 C11 A:28A306 4.6 30.0 1.0 N A:GLY81 4.7 25.9 1.0 HG3 A:GLU80 4.7 24.7 1.0 HB1 A:ALA20 4.7 33.4 1.0 CA A:GLU80 4.7 23.1 1.0 OH A:TYR24 4.9 52.7 1.0 HD12 A:LEU106 4.9 31.9 1.0 HD13 A:LEU106 4.9 31.9 1.0 CE2 A:TYR24 5.0 46.1 1.0 O A:ARG82 5.0 26.2 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