Manganese in PDB 6dcy: The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid, PDB code: 6dcy was solved by B.L.Dick, C.N.Morrison, S.M.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.77 / 2.08
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.540, 75.540, 120.360, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 27.1

The binding sites of Manganese atom in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid (pdb code 6dcy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid, PDB code: 6dcy:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:32.4 occ:1.00 OAH A:G5V303 2.0 37.0 1.0 OD2 A:ASP108 2.1 31.6 1.0 O A:ILE120 2.1 30.5 1.0 OE2 A:GLU119 2.1 32.5 1.0 NE2 A:HIS41 2.2 29.4 1.0 OAD A:G5V303 2.3 39.6 1.0 CAG A:G5V303 2.8 40.4 1.0 CAC A:G5V303 2.9 42.0 1.0 CG A:ASP108 3.0 32.4 1.0 CE1 A:HIS41 3.0 25.7 1.0 CD A:GLU119 3.2 34.2 1.0 OD1 A:ASP108 3.2 32.3 1.0 C A:ILE120 3.3 32.2 1.0 CD2 A:HIS41 3.3 27.6 1.0 OE1 A:GLU119 3.7 31.5 1.0 MN A:MN302 3.7 40.7 1.0 N A:ILE120 3.8 34.5 1.0 CA A:ILE120 4.0 34.5 1.0 O A:HOH403 4.1 28.5 1.0 NZ A:LYS134 4.1 38.5 1.0 CAF A:G5V303 4.1 48.6 1.0 ND1 A:HIS41 4.1 29.3 1.0 CB A:ILE120 4.3 35.2 1.0 CAB A:G5V303 4.3 47.3 1.0 CG A:GLU119 4.3 34.1 1.0 CG A:HIS41 4.4 27.5 1.0 CB A:ASP108 4.4 30.7 1.0 N A:GLY121 4.4 29.1 1.0 O A:HOH406 4.5 29.3 1.0 CE A:LYS134 4.6 38.0 1.0 CA A:GLY121 4.7 31.2 1.0 CAJ A:G5V303 4.7 47.4 1.0 C A:GLU119 4.7 33.9 1.0 OE2 A:GLU80 4.8 32.7 1.0 CG2 A:ILE120 4.9 37.6 1.0

Manganese binding site 2 out of 2 in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 5-Hydroxy-2-Methyl-4-Oxo-4H-Pyran-3-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:40.7 occ:1.00 OD1 A:ASP108 2.1 32.3 1.0 OE2 A:GLU80 2.2 32.7 1.0 O A:HOH403 2.3 28.5 1.0 OAH A:G5V303 2.3 37.0 1.0 O A:HOH404 2.3 37.1 1.0 OAL A:G5V303 2.4 46.0 1.0 CAJ A:G5V303 2.4 47.4 1.0 OAK A:G5V303 2.7 68.0 1.0 CAG A:G5V303 3.1 40.4 1.0 CAF A:G5V303 3.1 48.6 1.0 CG A:ASP108 3.2 32.4 1.0 CD A:GLU80 3.3 39.4 1.0 OD2 A:ASP108 3.7 31.6 1.0 MN A:MN301 3.7 32.4 1.0 CE1 A:HIS41 3.9 25.7 1.0 O A:LEU106 4.1 36.3 1.0 CG A:GLU80 4.1 36.6 1.0 O A:HOH408 4.1 42.2 1.0 O A:PRO107 4.1 29.6 1.0 OE1 A:GLU80 4.1 43.1 1.0 O A:HOH401 4.2 39.6 1.0 CB A:GLU80 4.2 36.6 1.0 OE1 A:GLU119 4.3 31.5 1.0 CB A:ASP108 4.3 30.7 1.0 CA A:ASP108 4.3 33.7 1.0 C A:PRO107 4.4 32.1 1.0 CAC A:G5V303 4.4 42.0 1.0 OE2 A:GLU119 4.4 32.5 1.0 CAE A:G5V303 4.5 47.7 1.0 N A:ASP108 4.5 32.5 1.0 NE2 A:HIS41 4.5 29.4 1.0 CD A:GLU119 4.8 34.2 1.0 CA A:GLU80 4.9 35.4 1.0 OAD A:G5V303 5.0 39.6 1.0 ND1 A:HIS41 5.0 29.3 1.0

C.V.Credille, B.L.Dick, C.N.Morrison, R.W.Stokes, R.N.Adamek, N.C.Wu, I.A.Wilson, S.M.Cohen. Structure-Activity Relationships in Metal-Binding Pharmacophores For Influenza Endonuclease. J. Med. Chem. V. 61 10206 2018.
ISSN: ISSN 1520-4804
PubMed: 30351002
DOI: 10.1021/ACS.JMEDCHEM.8B01363