Manganese in PDB 7dck: Crystal Structure of Phosphodiesterase TW9814

The structure of Crystal Structure of Phosphodiesterase TW9814, PDB code: 7dck was solved by Y.Heo, J.H.Yun, J.H.Park, S.B.Park, S.S.Cha, W.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.07 / 2.34
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	164.288, 164.288, 55.645, 90, 90, 120
R / Rfree (%)	17.9 / 20.9

The binding sites of Manganese atom in the Crystal Structure of Phosphodiesterase TW9814 (pdb code 7dck). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Phosphodiesterase TW9814, PDB code: 7dck:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Phosphodiesterase TW9814


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Phosphodiesterase TW9814 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:50.2 occ:1.00 ND1 A:HIS81 2.2 50.1 1.0 NE2 A:HIS79 2.2 46.7 1.0 NE2 A:HIS165 2.3 54.2 1.0 CE1 A:HIS81 3.0 50.9 1.0 CE1 A:HIS79 3.2 41.9 1.0 CD2 A:HIS79 3.2 40.6 1.0 CE1 A:HIS165 3.2 45.6 1.0 CG A:HIS81 3.2 43.8 1.0 CD2 A:HIS165 3.2 48.7 1.0 CB A:CYS163 3.4 43.7 1.0 MN A:MN302 3.6 65.5 1.0 CB A:HIS81 3.6 40.4 1.0 SG A:CYS163 3.8 44.2 1.0 NE2 A:HIS84 4.1 47.3 1.0 NE2 A:HIS81 4.2 46.9 1.0 ND1 A:HIS79 4.3 45.7 1.0 CD2 A:HIS81 4.3 44.6 1.0 CG A:HIS79 4.3 40.6 1.0 CD2 A:HIS84 4.3 41.4 1.0 ND1 A:HIS165 4.3 53.0 1.0 CG A:HIS165 4.4 55.1 1.0 OD1 A:ASP83 4.6 40.3 1.0 CA A:CYS163 4.8 53.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Phosphodiesterase TW9814


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Phosphodiesterase TW9814 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:65.5 occ:1.00 OD2 A:ASP83 2.2 40.4 1.0 NE2 A:HIS84 2.2 47.3 1.0 NE2 A:HIS219 2.3 45.5 1.0 CD2 A:HIS84 3.1 41.4 1.0 CG A:ASP83 3.1 38.3 1.0 CE1 A:HIS219 3.2 45.7 1.0 CE1 A:HIS84 3.3 43.3 1.0 CD2 A:HIS219 3.3 43.0 1.0 OD1 A:ASP83 3.4 40.3 1.0 SG A:CYS163 3.5 44.2 1.0 MN A:MN301 3.6 50.2 1.0 CB A:CYS163 3.8 43.7 1.0 CG A:HIS84 4.2 41.1 1.0 ND1 A:HIS84 4.3 43.2 1.0 ND1 A:HIS219 4.3 43.3 1.0 NE1 A:TRP34 4.4 41.0 1.0 CG A:HIS219 4.4 45.1 1.0 CB A:ASP83 4.4 40.9 1.0 CE1 A:HIS79 4.5 41.9 1.0 NE2 A:HIS79 4.5 46.7 1.0 SG A:CYS220 4.6 52.1 1.0 CA A:CYS163 4.8 53.0 1.0 CB A:CYS220 4.9 48.4 1.0 CD1 A:TRP34 4.9 47.5 1.0 O A:ASP83 5.0 40.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Phosphodiesterase TW9814


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Phosphodiesterase TW9814 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:80.1 occ:1.00 OD2 B:ASP83 2.2 45.5 1.0 NE2 B:HIS84 2.3 46.5 1.0 NE2 B:HIS219 2.3 42.6 1.0 CD2 B:HIS84 3.1 38.8 1.0 CD2 B:HIS219 3.2 42.4 1.0 CG B:ASP83 3.2 41.7 1.0 CE1 B:HIS84 3.4 40.9 1.0 CE1 B:HIS219 3.4 37.6 1.0 CB B:CYS163 3.5 38.2 1.0 MN B:MN302 3.5 46.8 1.0 OD1 B:ASP83 3.7 43.6 1.0 SG B:CYS163 3.7 48.3 1.0 CG B:HIS84 4.3 39.6 1.0 SG B:CYS220 4.3 48.8 1.0 ND1 B:HIS84 4.4 45.4 1.0 CG B:HIS219 4.4 42.5 1.0 CA B:CYS163 4.4 53.0 1.0 NE2 B:HIS79 4.5 44.9 1.0 ND1 B:HIS219 4.5 43.7 1.0 CE1 B:HIS79 4.5 42.9 1.0 CB B:ASP83 4.5 38.6 1.0 N B:CYS163 4.6 45.6 1.0 NE1 B:TRP34 4.7 39.7 1.0 CB B:CYS220 4.7 52.0 1.0 O B:GLY162 4.7 46.1 1.0 C B:GLY162 4.9 49.3 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Phosphodiesterase TW9814


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Phosphodiesterase TW9814 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:46.8 occ:1.00 ND1 B:HIS81 2.2 44.4 1.0 NE2 B:HIS165 2.2 50.2 1.0 NE2 B:HIS79 2.3 44.9 1.0 CE1 B:HIS81 3.0 41.4 1.0 CE1 B:HIS165 3.1 48.8 1.0 CD2 B:HIS79 3.2 44.5 1.0 CD2 B:HIS165 3.2 47.1 1.0 CB B:CYS163 3.3 38.2 1.0 CE1 B:HIS79 3.3 42.9 1.0 CG B:HIS81 3.3 41.7 1.0 MN B:MN301 3.5 80.1 1.0 CB B:HIS81 3.7 40.4 1.0 SG B:CYS163 3.9 48.3 1.0 NE2 B:HIS81 4.2 41.0 1.0 ND1 B:HIS165 4.2 46.0 1.0 NE2 B:HIS84 4.3 46.5 1.0 CD2 B:HIS81 4.3 36.4 1.0 CG B:HIS165 4.3 46.9 1.0 ND1 B:HIS79 4.4 46.6 1.0 CG B:HIS79 4.4 46.1 1.0 CD2 B:HIS84 4.4 38.8 1.0 OD1 B:ASP83 4.6 43.6 1.0 CA B:CYS163 4.7 53.0 1.0 OD2 B:ASP83 4.8 45.5 1.0 N B:CYS163 4.9 45.6 1.0

Y.Heo, J.H.Yun, J.H.Park, S.B.Park, S.S.Cha, W.Lee. Crystal Structure of Phosphodiesterase TW9814 To Be Published.