Cobalt in PDB 3n5f: Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43

All present enzymatic activity of Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43:
3.5.1.87;

The structure of Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43, PDB code: 3n5f was solved by A.Garcia-Pino, S.Martinez-Rodriguez, J.A.Gavira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.208, 211.683, 43.091, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 27.6

The structure of Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43 also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Cobalt atom in the Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43 (pdb code 3n5f). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43, PDB code: 3n5f:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co410 b:19.1 occ:1.00 NE2 A:HIS79 2.1 19.2 1.0 OD2 A:ASP90 2.2 20.9 1.0 NE2 A:HIS189 2.3 7.5 1.0 CD2 A:HIS79 3.0 18.3 1.0 CE1 A:HIS79 3.1 20.1 1.0 CE1 A:HIS189 3.2 9.2 1.0 CG A:ASP90 3.3 19.6 1.0 CD2 A:HIS189 3.3 9.0 1.0 OE1 A:GLU124 3.5 29.0 1.0 OE2 A:GLU124 3.6 28.5 1.0 OD1 A:ASP90 3.7 22.6 1.0 CD2 A:HIS356 3.7 15.1 1.0 CD A:GLU124 3.8 28.9 1.0 OE2 A:GLU125 3.9 30.4 1.0 CG A:HIS79 4.1 17.2 1.0 ND1 A:HIS79 4.1 20.4 1.0 NE2 A:HIS356 4.2 15.5 1.0 ND1 A:HIS189 4.4 7.6 1.0 N A:GLY91 4.4 16.9 1.0 CG A:HIS189 4.4 9.3 1.0 C A:ASP90 4.6 18.1 1.0 CB A:ASP90 4.6 19.1 1.0 OG A:SER78 4.8 12.7 1.0 CA A:GLY91 4.8 16.0 1.0 CD A:GLU125 4.8 31.2 1.0 CA A:ASP90 4.9 18.9 1.0 NE2 A:GLN192 4.9 11.8 1.0 OE1 A:GLU187 4.9 13.0 1.0 O A:HOH446 4.9 17.0 1.0 CG A:GLU124 4.9 27.9 1.0 CG A:HIS356 4.9 15.7 1.0 O A:ASP90 5.0 18.5 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of L-N-Carbamoylase From Geobacillus Stearothermophilus CECT43 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co411 b:9.2 occ:1.00 OD2 B:ASP90 2.1 6.5 1.0 NE2 B:HIS189 2.2 2.0 1.0 NE2 B:HIS79 2.3 7.2 1.0 CG B:ASP90 3.1 7.5 1.0 CE1 B:HIS189 3.1 2.0 1.0 CD2 B:HIS79 3.2 5.8 1.0 O B:HOH481 3.2 32.1 1.0 CD2 B:HIS189 3.3 2.7 1.0 OD1 B:ASP90 3.4 7.9 1.0 CE1 B:HIS79 3.4 6.5 1.0 OE2 B:GLU124 3.6 13.6 1.0 OE2 B:GLU125 4.1 19.3 1.0 CD B:GLU124 4.2 12.5 1.0 ND1 B:HIS356 4.2 5.0 1.0 O B:HOH412 4.2 8.6 1.0 ND1 B:HIS189 4.2 2.0 1.0 N B:GLY91 4.3 5.5 1.0 CG B:HIS79 4.4 6.0 1.0 CG B:HIS189 4.4 3.6 1.0 C B:ASP90 4.4 7.1 1.0 ND1 B:HIS79 4.4 5.2 1.0 CB B:ASP90 4.4 6.9 1.0 CD B:GLU125 4.6 18.3 1.0 OE1 B:GLU124 4.6 12.9 1.0 CA B:ASP90 4.7 7.5 1.0 O B:ASP90 4.7 8.0 1.0 CA B:GLY91 4.8 3.8 1.0 CE1 B:HIS356 4.8 5.7 1.0 OE1 B:GLU125 4.8 18.7 1.0 OE1 B:GLU187 4.9 2.0 1.0 OG B:SER78 4.9 7.5 1.0 CG B:GLU124 5.0 11.7 1.0

S.Martinez-Rodriguez, A.Garcia-Pino, F.J.Las Heras-Vazquez, J.M.Clemente-Jimenez, F.Rodriguez-Vico, J.M.Garcia-Ruiz, R.Loris, J.A.Gavira. Mutational and Structural Analysis of L-N-Carbamoylase Reveals New Insights Into A Peptidase M20/M25/M40 Family Member. J.Bacteriol. V. 194 5759 2012.
ISSN: ISSN 0021-9193
PubMed: 22904279
DOI: 10.1128/JB.01056-12