Manganese in PDB 5o25: Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State

The structure of Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State, PDB code: 5o25 was solved by G.Witte, D.Drexler, M.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.31 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.670, 54.930, 108.640, 90.00, 118.03, 90.00
R / Rfree (%)	16.4 / 19

The structure of Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State (pdb code 5o25). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State, PDB code: 5o25:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:24.7 occ:0.67 O A:HOH599 2.0 23.3 1.0 OD2 A:ASP80 2.1 21.0 1.0 O A:HOH703 2.1 32.5 1.0 OD2 A:ASP23 2.3 19.4 1.0 NE2 A:HIS19 2.4 23.6 1.0 OD1 A:ASP23 2.4 18.5 1.0 CG A:ASP23 2.7 20.4 1.0 CG A:ASP80 3.1 17.8 1.0 CD2 A:HIS19 3.2 24.0 1.0 OD1 A:ASP80 3.4 16.2 1.0 MN A:MN402 3.4 23.1 0.7 O A:HOH658 3.4 33.4 1.0 CE1 A:HIS19 3.4 23.4 1.0 CB A:ASP25 4.0 16.6 1.0 N A:CYS26 4.1 16.2 1.0 CB A:ASP23 4.2 20.5 1.0 O A:HOH678 4.3 43.0 1.0 O A:ASP80 4.3 19.1 1.0 CG A:HIS19 4.4 23.0 1.0 CB A:ASP80 4.4 17.3 1.0 ND1 A:HIS19 4.5 23.6 1.0 CB A:CYS26 4.5 17.9 1.0 OD1 A:ASP154 4.5 19.5 1.0 OD2 A:ASP25 4.6 20.3 1.0 CA A:CYS26 4.7 15.2 1.0 C A:ASP25 4.7 16.8 1.0 CA A:ASP25 4.8 16.8 1.0 CG A:ASP25 4.8 17.0 1.0 O A:HOH532 4.8 17.3 1.0 N A:ASP23 4.8 17.5 1.0 OD2 A:ASP154 4.9 23.6 1.0 N A:ASP25 4.9 15.6 1.0 CE1 A:HIS105 5.0 44.9 1.0 CA A:ASP23 5.0 18.9 1.0

Manganese binding site 2 out of 4 in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:23.1 occ:0.70 O A:HOH599 1.9 23.3 1.0 OD2 A:ASP25 2.1 20.3 1.0 OD1 A:ASP80 2.2 16.2 1.0 OD2 A:ASP154 2.3 23.6 1.0 NE2 A:HIS104 2.3 19.3 1.0 O A:HOH658 2.5 33.4 1.0 CG A:ASP25 3.1 17.0 1.0 CE1 A:HIS104 3.1 17.4 1.0 CG A:ASP80 3.1 17.8 1.0 CG A:ASP154 3.3 23.6 1.0 CB A:ASP25 3.4 16.6 1.0 OD2 A:ASP80 3.4 21.0 1.0 MN A:MN401 3.4 24.7 0.7 CD2 A:HIS104 3.4 18.2 1.0 OD1 A:ASP154 3.6 19.5 1.0 O A:HOH703 3.9 32.5 1.0 OG1 A:THR124 4.1 16.6 1.0 N A:THR124 4.2 13.6 1.0 OD1 A:ASP25 4.2 16.8 1.0 ND1 A:HIS104 4.3 18.8 1.0 CE1 A:HIS105 4.4 44.9 1.0 CB A:ASP80 4.5 17.3 1.0 CG A:HIS104 4.5 18.4 1.0 NE2 A:HIS286 4.5 40.5 1.0 CB A:ASP154 4.5 17.8 1.0 CA A:ALA123 4.7 17.8 1.0 CB A:THR124 4.7 14.9 1.0 NE2 A:HIS105 4.8 46.2 1.0 CA A:ASP25 4.8 16.8 1.0 CE1 A:HIS286 5.0 41.5 1.0

Manganese binding site 3 out of 4 in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:46.4 occ:0.67 O B:HOH546 2.2 32.6 1.0 OD2 B:ASP80 2.2 31.4 1.0 OD1 B:ASP23 2.4 32.0 1.0 OD2 B:ASP23 2.5 38.9 1.0 NE2 B:HIS19 2.6 39.7 1.0 CG B:ASP23 2.8 31.1 1.0 O B:HOH606 2.8 42.4 1.0 CG B:ASP80 3.2 24.0 1.0 MN B:MN404 3.3 27.9 0.7 CE1 B:HIS19 3.5 42.2 1.0 O B:HOH597 3.6 43.9 1.0 OD1 B:ASP80 3.6 24.2 1.0 CD2 B:HIS19 3.6 40.3 1.0 CB B:ASP25 3.8 23.2 1.0 N B:CYS26 3.9 18.6 1.0 CB B:ASP23 4.3 26.5 1.0 CB B:CYS26 4.3 24.7 1.0 OD1 B:ASP154 4.4 30.1 1.0 C B:ASP25 4.5 19.8 1.0 OD2 B:ASP25 4.5 25.8 1.0 CA B:CYS26 4.5 21.7 1.0 CB B:ASP80 4.5 21.9 1.0 CA B:ASP25 4.5 20.4 1.0 O B:ASP80 4.6 26.6 1.0 CG B:ASP25 4.6 23.5 1.0 ND1 B:HIS19 4.7 40.6 1.0 O B:HOH571 4.7 18.4 1.0 N B:ASP25 4.7 18.8 1.0 CG B:HIS19 4.8 38.5 1.0 CE1 B:HIS105 4.8 49.4 1.0 N B:ASP23 5.0 23.0 1.0 OD2 B:ASP154 5.0 37.0 1.0

Manganese binding site 4 out of 4 in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn404 b:27.9 occ:0.66 O B:HOH546 2.1 32.6 1.0 OD2 B:ASP25 2.1 25.8 1.0 NE2 B:HIS104 2.3 33.1 1.0 OD1 B:ASP80 2.3 24.2 1.0 OD2 B:ASP154 2.4 37.0 1.0 CG B:ASP25 3.1 23.5 1.0 CG B:ASP80 3.2 24.0 1.0 CD2 B:HIS104 3.2 33.1 1.0 CE1 B:HIS104 3.3 31.4 1.0 CG B:ASP154 3.3 32.5 1.0 OD2 B:ASP80 3.3 31.4 1.0 MN B:MN403 3.3 46.4 0.7 CB B:ASP25 3.4 23.2 1.0 OD1 B:ASP154 3.5 30.1 1.0 O B:HOH606 3.5 42.4 1.0 CE1 B:HIS105 3.7 49.4 1.0 NE2 B:HIS105 4.1 46.7 1.0 OG1 B:THR124 4.1 19.6 1.0 N B:THR124 4.2 19.0 1.0 OD1 B:ASP25 4.3 18.0 1.0 O B:HOH597 4.3 43.9 1.0 ND1 B:HIS104 4.4 32.6 1.0 CG B:HIS104 4.4 31.7 1.0 CB B:ASP80 4.6 21.9 1.0 CA B:ALA123 4.7 19.5 1.0 CB B:ASP154 4.7 22.6 1.0 ND1 B:HIS105 4.7 47.0 1.0 CB B:THR124 4.7 16.8 1.0 CA B:ASP25 4.8 20.4 1.0 C B:ALA123 5.0 19.2 1.0 O B:ALA122 5.0 23.1 1.0

D.J.Drexler, M.Muller, C.A.Rojas-Cordova, A.M.Bandera, G.Witte. Structural and Biophysical Analysis of the Soluble Dhh/DHHA1-Type Phosphodiesterase TM1595 From Thermotoga Maritima. Structure V. 25 1887 2017.
ISSN: ISSN 1878-4186
PubMed: 29107484
DOI: 10.1016/J.STR.2017.10.001