Manganese in PDB 4yyl: Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease

The structure of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease, PDB code: 4yyl was solved by S.Fudo, N.Yamamoto, M.Nukaga, T.Odagiri, M.Tashiro, S.Neya, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.27 / 1.91
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.766, 66.766, 126.251, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.4

The structure of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Manganese atom in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease (pdb code 4yyl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease, PDB code: 4yyl:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:37.3 occ:1.00 OAH A:4KN301 2.0 36.2 1.0 OE2 A:GLU119 2.0 38.0 1.0 OD2 A:ASP108 2.2 28.7 1.0 OAI A:4KN301 2.3 39.9 1.0 O A:ILE120 2.3 30.6 1.0 NE2 A:HIS41 2.3 34.2 1.0 CAE A:4KN301 3.0 51.2 1.0 CG A:ASP108 3.1 35.3 1.0 CE1 A:HIS41 3.1 32.3 1.0 CAF A:4KN301 3.1 57.7 1.0 CD A:GLU119 3.1 40.0 1.0 OD1 A:ASP108 3.3 29.1 1.0 CD2 A:HIS41 3.4 30.8 1.0 C A:ILE120 3.5 30.4 1.0 MN A:MN305 3.7 32.5 1.0 OE1 A:GLU119 3.7 34.3 1.0 N A:ILE120 3.8 27.4 1.0 CAA A:4KN302 3.8 59.7 1.0 O A:HOH433 3.9 33.1 1.0 NZ A:LYS134 4.0 40.7 1.0 CAB A:4KN302 4.0 57.0 1.0 CA A:ILE120 4.1 24.5 1.0 ND1 A:HIS41 4.2 29.0 1.0 CAD A:4KN301 4.3 55.0 1.0 CG A:GLU119 4.3 34.4 1.0 CB A:ILE120 4.3 27.2 1.0 CG A:HIS41 4.4 28.1 1.0 CB A:ASP108 4.5 25.1 1.0 CAA A:4KN301 4.5 62.0 1.0 N A:GLY121 4.5 28.9 1.0 OE1 A:GLU80 4.5 35.7 1.0 C A:GLU119 4.7 28.1 1.0 CA A:GLY121 4.7 33.2 1.0 OAG A:4KN301 4.8 40.0 1.0 CE A:LYS134 4.9 43.5 1.0 CAF A:4KN302 4.9 48.5 1.0

Manganese binding site 2 out of 2 in the Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phenolic Acid Derivative Bound to Influenza Strain H1N1 Polymerase Subunit Pa Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn305 b:32.5 occ:1.00 O A:HOH433 1.9 33.1 1.0 OE1 A:GLU80 2.0 35.7 1.0 OAH A:4KN301 2.1 36.2 1.0 OD1 A:ASP108 2.2 29.1 1.0 OAG A:4KN301 2.2 40.0 1.0 O A:HOH455 2.3 35.2 1.0 CAE A:4KN301 2.9 51.2 1.0 CAD A:4KN301 2.9 55.0 1.0 CD A:GLU80 3.1 36.2 1.0 CG A:ASP108 3.2 35.3 1.0 OD2 A:ASP108 3.7 28.7 1.0 MN A:MN304 3.7 37.3 1.0 CE1 A:HIS41 3.9 32.3 1.0 OE2 A:GLU80 4.0 36.6 1.0 CG A:GLU80 4.1 34.1 1.0 O A:HOH531 4.1 44.5 1.0 O A:PRO107 4.1 32.8 1.0 CAF A:4KN301 4.2 57.7 1.0 O A:LEU106 4.2 36.2 1.0 CAC A:4KN301 4.3 65.3 1.0 CB A:GLU80 4.3 31.6 1.0 OE1 A:GLU119 4.3 34.3 1.0 C A:PRO107 4.4 31.3 1.0 CB A:ASP108 4.4 25.1 1.0 CA A:ASP108 4.4 25.6 1.0 NE2 A:HIS41 4.4 34.2 1.0 OE2 A:GLU119 4.5 38.0 1.0 OAK A:4KN301 4.6 70.5 1.0 N A:ASP108 4.6 27.7 1.0 OAI A:4KN301 4.7 39.9 1.0 CAL A:4KN302 4.8 54.3 1.0 CD A:GLU119 4.9 40.0 1.0 OAM A:4KN302 4.9 63.5 1.0 CAJ A:4KN301 4.9 75.0 1.0 CA A:GLU80 4.9 31.1 1.0 ND1 A:HIS41 4.9 29.0 1.0

S.Fudo, N.Yamamoto, M.Nukaga, T.Odagiri, M.Tashiro, S.Neya, T.Hoshino. Structural and Computational Study on the Inhibitory Compounds For Endonuclease Activity of Influenza Virus Polymerase To Be Published.