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

The structure of The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 3-Hydroxy-4-Oxo-4H-Pyran-2-Carboxylic Acid, PDB code: 6dcz 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)	28.89 / 2.89
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	75.840, 75.840, 121.300, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 27.6

The binding sites of Manganese atom in the The N-Terminal Domain of Pa Endonuclease From the Influenza H1N1 Virus in Complex with 3-Hydroxy-4-Oxo-4H-Pyran-2-Carboxylic Acid (pdb code 6dcz). 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 3-Hydroxy-4-Oxo-4H-Pyran-2-Carboxylic Acid, PDB code: 6dcz:
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 3-Hydroxy-4-Oxo-4H-Pyran-2-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 3-Hydroxy-4-Oxo-4H-Pyran-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:34.4 occ:1.00 OE1 A:GLU80 1.9 39.7 1.0 OAJ A:G5Y301 1.9 34.7 1.0 OAI A:G5Y301 2.0 35.3 1.0 OD1 A:ASP108 2.1 26.7 1.0 O A:HOH402 2.2 24.7 1.0 O A:HOH401 2.3 21.6 1.0 CAH A:G5Y301 3.0 35.4 1.0 CAF A:G5Y301 3.0 34.9 1.0 CD A:GLU80 3.0 39.3 1.0 CG A:ASP108 3.2 26.3 1.0 CAG A:G5Y301 3.3 35.5 1.0 MN A:MN303 3.7 29.2 1.0 OD2 A:ASP108 3.7 25.2 1.0 OE2 A:GLU80 3.7 41.6 1.0 CE1 A:HIS41 3.8 21.6 1.0 CG A:GLU80 4.0 38.5 1.0 OAK A:G5Y301 4.1 35.6 1.0 O A:LEU106 4.2 32.8 1.0 CAE A:G5Y301 4.2 35.6 1.0 OE1 A:GLU119 4.2 28.5 1.0 OE2 A:GLU119 4.3 28.9 1.0 CB A:GLU80 4.3 39.5 1.0 CB A:ASP108 4.4 27.5 1.0 NE2 A:HIS41 4.5 21.5 1.0 CA A:ASP108 4.5 29.1 1.0 OAD A:G5Y301 4.6 35.6 1.0 C A:PRO107 4.6 29.6 1.0 N A:ASP108 4.6 29.6 1.0 CD A:GLU119 4.7 30.4 1.0 OAC A:G5Y301 4.7 36.6 1.0 O A:PRO107 4.8 27.2 1.0 O A:HOH404 4.8 24.2 1.0 ND1 A:HIS41 4.8 20.9 1.0 CA A:GLU80 4.9 39.0 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 3-Hydroxy-4-Oxo-4H-Pyran-2-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 3-Hydroxy-4-Oxo-4H-Pyran-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:29.2 occ:1.00 OD2 A:ASP108 2.0 25.2 1.0 OAD A:G5Y301 2.0 35.6 1.0 OE2 A:GLU119 2.1 28.9 1.0 O A:ILE120 2.1 29.4 1.0 NE2 A:HIS41 2.2 21.5 1.0 OAJ A:G5Y301 2.3 34.7 1.0 CAE A:G5Y301 2.8 35.6 1.0 CE1 A:HIS41 2.9 21.6 1.0 CG A:ASP108 2.9 26.3 1.0 CAF A:G5Y301 3.0 34.9 1.0 CD A:GLU119 3.1 30.4 1.0 OD1 A:ASP108 3.2 26.7 1.0 C A:ILE120 3.3 29.3 1.0 CD2 A:HIS41 3.3 21.7 1.0 N A:ILE120 3.6 29.4 1.0 MN A:MN302 3.7 34.4 1.0 OE1 A:GLU119 3.7 28.5 1.0 CA A:ILE120 3.8 30.7 1.0 ND1 A:HIS41 4.1 20.9 1.0 O A:HOH402 4.1 24.7 1.0 CB A:ILE120 4.1 32.3 1.0 CAA A:G5Y301 4.1 35.2 1.0 CG A:GLU119 4.3 31.1 1.0 CB A:ASP108 4.3 27.5 1.0 CG A:HIS41 4.3 21.4 1.0 CAG A:G5Y301 4.3 35.5 1.0 N A:GLY121 4.4 28.0 1.0 NZ A:LYS134 4.4 61.4 1.0 OE1 A:GLU80 4.5 39.7 1.0 C A:GLU119 4.6 30.1 1.0 CE A:LYS134 4.6 58.9 1.0 CA A:GLY121 4.8 27.3 1.0 O A:HOH404 4.8 24.2 1.0 CG2 A:ILE120 4.9 32.4 1.0 SG A:CYS45 4.9 33.3 1.0 CA A:GLU119 4.9 31.7 1.0 OAI A:G5Y301 5.0 35.3 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