Calcium 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:

Manganese

(Mn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State, PDB code: 5o25:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Wildtype T.Maritima Pde (TM1595) in Ligand-Free State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca401 b:52.8 occ:1.00 O B:GLY41 2.2 36.6 1.0 O B:HOH514 2.2 27.7 1.0 O B:HOH594 2.3 40.1 1.0 C B:GLY41 3.4 28.8 1.0 OD1 B:ASP12 3.7 31.4 1.0 OD2 B:ASP12 3.9 30.2 1.0 O B:HOH713 3.9 40.7 1.0 CA B:GLY41 4.1 25.9 1.0 CG B:ASP12 4.2 34.4 1.0 N B:LYS42 4.4 25.1 1.0 CA B:LYS42 4.5 25.6 1.0 C B:LYS42 4.7 24.4 1.0 N B:GLU43 4.9 24.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca402 b:45.7 occ:1.00 O B:HOH588 2.2 28.5 1.0 O B:HOH523 2.2 30.9 1.0 O B:HOH507 2.3 35.4 1.0 O B:HOH723 2.3 22.5 1.0 O B:HOH746 2.4 40.2 1.0 OE1 B:GLU57 3.8 26.1 1.0 O B:HOH570 3.9 24.1 1.0 O B:HOH650 4.0 38.4 1.0 O B:HOH535 4.0 27.5 1.0 OE2 B:GLU57 4.1 27.1 1.0 NZ B:LYS51 4.1 51.3 1.0 O B:HOH605 4.2 33.1 1.0 O B:ILE52 4.4 25.1 1.0 CD B:GLU57 4.4 24.9 1.0 O B:HOH708 4.5 34.2 1.0 CB B:ILE52 4.9 21.5 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