Calcium in PDB 8ryi: Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site

The structure of Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site, PDB code: 8ryi was solved by J.R.Fleming, H.Lutz, A.Bachmann, O.Mayans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.97 / 2.06
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.99, 86.52, 168.41, 90, 113.99, 90
R / Rfree (%)	16.9 / 19.9

The structure of Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Calcium atom in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site (pdb code 8ryi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site, PDB code: 8ryi:

Calcium binding site 1 out of 1 in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca405 b:37.9 occ:1.00 OD1 E:ASP3 2.3 45.6 1.0 O E:ALA0 2.3 43.7 1.0 O E:HOH522 2.5 43.2 1.0 O E:ASP3 2.5 44.5 1.0 C E:ASP3 3.4 45.1 1.0 C E:ALA0 3.5 43.7 1.0 CG E:ASP3 3.5 46.4 1.0 N E:ASP3 4.1 45.2 1.0 CA E:ASP3 4.1 45.1 1.0 N E:ARG4 4.2 52.9 1.0 CA E:ALA0 4.3 44.6 1.0 NH2 E:ARG4 4.3 59.8 1.0 N E:LYS5 4.4 41.5 1.0 OD2 E:ASP3 4.4 48.0 1.0 NZ E:LYS5 4.4 42.2 1.0 CA E:ARG4 4.4 52.6 1.0 CB E:ASP3 4.4 43.9 1.0 N E:MET1 4.5 49.1 1.0 C E:MET1 4.5 50.0 1.0 CA E:MET1 4.6 49.9 1.0 O E:MET1 4.6 51.7 1.0 CG E:LYS5 4.8 40.8 1.0 NE E:ARG4 4.8 59.1 1.0 C E:LEU2 4.9 50.3 1.0 CB E:ALA0 4.9 44.4 1.0 O E:HOH506 4.9 46.9 1.0 N E:LEU2 5.0 48.0 1.0 C E:ARG4 5.0 50.9 1.0

M.Sinn, L.Riede, J.R.Fleming, O.Mayans, D.Funck, J.S.Hartig. Metformin Hydrolase Is A Recently Evolved, Nickel-Dependent, Heteromeric Ureohydrolase To Be Published.