Nickel 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:

Calcium

(Ca)

1 atom

The binding sites of Nickel 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 Nickel atom.
In total 4 binding sites of Nickel where determined in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site, PDB code: 8ryi:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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 B:Ni403 b:49.3 occ:1.00 OD2 B:ASP183 2.1 38.5 1.0 ND1 B:HIS158 2.1 39.2 1.0 OD2 B:ASP187 2.2 43.2 1.0 O B:URE402 2.3 56.8 1.0 OD2 B:ASP276 2.5 40.8 1.0 CG B:ASP187 3.0 43.8 1.0 CE1 B:HIS158 3.1 40.1 1.0 CG B:ASP183 3.1 38.0 1.0 CG B:HIS158 3.2 39.3 1.0 C B:URE402 3.2 68.0 1.0 NI B:NI404 3.2 58.9 1.0 OD1 B:ASP187 3.2 42.9 1.0 OD1 B:ASP183 3.3 37.6 1.0 CB B:HIS158 3.5 38.2 1.0 CG B:ASP276 3.5 39.6 1.0 N2 B:URE402 3.7 62.0 1.0 CB B:ASP276 3.8 39.2 1.0 N1 B:URE402 4.1 66.2 1.0 NE2 B:HIS181 4.2 40.8 1.0 NE2 B:HIS158 4.2 39.5 1.0 CD2 B:HIS158 4.3 38.3 1.0 O B:ASN199 4.3 42.9 1.0 CB B:ASP187 4.4 42.0 1.0 O B:HOH601 4.4 34.8 1.0 CB B:ASP183 4.4 37.1 1.0 OD1 B:ASP276 4.6 40.0 1.0 CE1 B:HIS181 4.8 40.0 1.0 CB B:HIS185 4.9 40.8 1.0 OE2 B:GLU320 4.9 41.3 1.0 O B:HIS185 4.9 38.1 1.0

Nickel binding site 2 out of 4 in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni404 b:58.9 occ:1.00 OD2 B:ASP278 2.2 42.4 1.0 O B:URE402 2.3 56.8 1.0 OD1 B:ASP183 2.3 37.6 1.0 OD2 B:ASP276 2.4 40.8 1.0 ND1 B:HIS185 2.4 41.3 1.0 OD1 B:ASP278 2.5 41.0 1.0 CG B:ASP278 2.7 42.0 1.0 N2 B:URE402 2.8 62.0 1.0 C B:URE402 2.9 68.0 1.0 CG B:ASP276 3.1 39.6 1.0 NI B:NI403 3.2 49.3 1.0 CG B:ASP183 3.2 38.0 1.0 CE1 B:HIS185 3.3 41.0 1.0 CG B:HIS185 3.4 40.3 1.0 OD2 B:ASP183 3.5 38.5 1.0 CB B:HIS185 3.7 40.8 1.0 OD1 B:ASP276 3.7 40.0 1.0 CB B:ASP276 4.0 39.2 1.0 N B:HIS185 4.1 39.6 1.0 N1 B:URE402 4.1 66.2 1.0 CB B:ASP278 4.2 40.2 1.0 N B:CYS184 4.4 40.8 1.0 NE2 B:HIS185 4.5 40.9 1.0 CD2 B:HIS185 4.5 42.2 1.0 CA B:HIS185 4.6 40.2 1.0 OD1 B:ASP187 4.6 42.9 1.0 CB B:ASP183 4.6 37.1 1.0 CB B:CYS184 4.8 42.0 1.0 CA B:CYS184 4.9 41.3 1.0 C B:CYS184 4.9 43.1 1.0 ND1 B:HIS158 5.0 39.2 1.0 OD2 B:ASP187 5.0 43.2 1.0

Nickel binding site 3 out of 4 in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 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:Ni403 b:56.0 occ:1.00 OD2 E:ASP183 2.1 45.4 1.0 ND1 E:HIS158 2.1 43.4 1.0 OD2 E:ASP187 2.2 48.2 1.0 O E:URE402 2.5 83.7 1.0 OD2 E:ASP276 2.5 48.9 1.0 CG E:ASP187 3.0 48.9 1.0 CE1 E:HIS158 3.0 44.2 1.0 CG E:ASP183 3.0 44.6 1.0 NI E:NI404 3.1 63.6 1.0 CG E:HIS158 3.2 43.3 1.0 OD1 E:ASP187 3.2 48.5 1.0 C E:URE402 3.3 84.9 1.0 OD1 E:ASP183 3.4 44.0 1.0 CG E:ASP276 3.5 47.6 1.0 CB E:HIS158 3.5 42.8 1.0 N2 E:URE402 3.7 82.7 1.0 CB E:ASP276 3.8 45.9 1.0 NE2 E:HIS181 4.2 48.3 1.0 NE2 E:HIS158 4.2 44.0 1.0 CD2 E:HIS158 4.3 43.5 1.0 O E:ASN199 4.3 49.4 1.0 N1 E:URE402 4.3 84.7 1.0 CB E:ASP187 4.3 49.9 1.0 CB E:ASP183 4.4 43.9 1.0 O E:HOH633 4.5 44.0 1.0 OD1 E:ASP276 4.6 46.9 1.0 CE1 E:HIS181 4.7 49.4 1.0 OE2 E:GLU320 4.8 48.1 1.0 CB E:HIS185 4.9 46.8 1.0 OD2 E:ASP278 4.9 49.4 1.0 O E:HIS185 4.9 47.2 1.0

Nickel binding site 4 out of 4 in the Metformin Hydrolase From Aminobacter Niigataensis MD1 with Urea in the Active Site


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 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:Ni404 b:63.6 occ:1.00 OD2 E:ASP278 2.1 49.4 1.0 OD1 E:ASP183 2.3 44.0 1.0 O E:URE402 2.4 83.7 1.0 ND1 E:HIS185 2.4 47.2 1.0 OD2 E:ASP276 2.5 48.9 1.0 OD1 E:ASP278 2.6 45.1 1.0 CG E:ASP278 2.7 46.4 1.0 NI E:NI403 3.1 56.0 1.0 C E:URE402 3.1 84.9 1.0 CG E:ASP183 3.2 44.6 1.0 N2 E:URE402 3.2 82.7 1.0 CG E:ASP276 3.3 47.6 1.0 CE1 E:HIS185 3.4 49.1 1.0 CG E:HIS185 3.4 46.2 1.0 OD2 E:ASP183 3.4 45.4 1.0 CB E:HIS185 3.6 46.8 1.0 OD1 E:ASP276 3.9 46.9 1.0 O E:HOH544 4.0 61.2 1.0 N E:HIS185 4.1 47.4 1.0 CB E:ASP276 4.1 45.9 1.0 CB E:ASP278 4.2 45.6 1.0 N1 E:URE402 4.4 84.7 1.0 OD1 E:ASP187 4.4 48.5 1.0 N E:CYS184 4.5 48.1 1.0 CA E:HIS185 4.5 49.2 1.0 NE2 E:HIS185 4.5 49.4 1.0 CD2 E:HIS185 4.5 48.9 1.0 CB E:ASP183 4.6 43.9 1.0 OD2 E:ASP187 4.9 48.2 1.0 ND1 E:HIS158 4.9 43.4 1.0 CB E:CYS184 5.0 49.8 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.