Cobalt in PDB 6n9r: Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl, PDB code: 6n9r was solved by C.Bergonzi, M.Schwab, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.80 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.010, 108.590, 78.600, 90.00, 115.75, 90.00
R / Rfree (%)	17.6 / 23.5

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl also contains other interesting chemical elements:

Iron

(Fe)

3 atoms

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl (pdb code 6n9r). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl, PDB code: 6n9r:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:13.7 occ:1.00 O A:HOH401 1.9 20.4 1.0 NE2 A:HIS118 2.1 9.4 1.0 NE2 A:HIS198 2.1 12.8 1.0 ND1 A:HIS120 2.2 17.0 1.0 OD2 A:ASP220 2.4 21.4 1.0 O6 A:OHN303 2.5 26.1 0.7 CD2 A:HIS118 3.0 11.8 1.0 CD2 A:HIS198 3.0 13.1 1.0 CE1 A:HIS120 3.1 16.8 1.0 CG A:HIS120 3.2 13.9 1.0 CE1 A:HIS118 3.2 15.2 1.0 CE1 A:HIS198 3.2 19.3 1.0 C2 A:OHN303 3.4 31.9 0.7 CG A:ASP220 3.4 16.8 1.0 CB A:HIS120 3.5 12.9 1.0 FE A:FE302 3.6 18.0 1.0 CB A:ASP220 3.7 13.2 1.0 OAP A:OHN303 3.8 18.1 0.7 CD2 A:HIS123 4.1 14.7 1.0 NE2 A:HIS123 4.1 12.1 1.0 CG A:HIS118 4.2 14.0 1.0 CG A:HIS198 4.2 11.7 1.0 NE2 A:HIS120 4.3 15.9 1.0 ND1 A:HIS118 4.3 14.1 1.0 ND1 A:HIS198 4.3 13.8 1.0 CD2 A:HIS120 4.3 15.6 1.0 OD1 A:ASP122 4.3 16.9 1.0 O9 A:OHN303 4.5 45.3 0.7 C1 A:OHN303 4.5 32.7 0.7 OD1 A:ASP220 4.6 18.5 1.0 OH A:TYR223 4.8 19.9 1.0 OD2 A:ASP122 4.9 19.0 1.0 CA A:HIS120 4.9 13.5 1.0

Cobalt binding site 2 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ P:Co301 b:14.0 occ:1.00 O P:HOH402 1.8 19.9 1.0 ND1 P:HIS120 2.1 14.3 1.0 NE2 P:HIS198 2.1 13.3 1.0 NE2 P:HIS118 2.1 12.6 1.0 OD2 P:ASP220 2.4 21.8 1.0 O6 P:OHN308 2.6 45.7 0.7 CD2 P:HIS118 2.9 14.8 1.0 CD2 P:HIS198 3.0 13.3 1.0 CE1 P:HIS120 3.0 18.6 1.0 CG P:HIS120 3.1 15.8 1.0 CE1 P:HIS198 3.1 14.5 1.0 CE1 P:HIS118 3.2 14.6 1.0 CB P:HIS120 3.4 15.8 1.0 CG P:ASP220 3.4 17.1 1.0 C2 P:OHN308 3.5 46.7 0.7 FE P:FE302 3.6 18.9 1.0 CB P:ASP220 3.8 15.9 1.0 OAP P:OHN308 4.0 24.7 0.7 CG P:HIS118 4.1 13.5 1.0 CG P:HIS198 4.1 11.4 1.0 NE2 P:HIS120 4.1 17.0 1.0 CD2 P:HIS123 4.2 15.6 1.0 ND1 P:HIS198 4.2 13.0 1.0 CD2 P:HIS120 4.2 15.8 1.0 ND1 P:HIS118 4.2 14.9 1.0 NE2 P:HIS123 4.2 15.8 1.0 O9 P:OHN308 4.2 64.3 0.7 OD1 P:ASP122 4.3 19.0 1.0 C1 P:OHN308 4.5 41.8 0.7 OD1 P:ASP220 4.6 18.4 1.0 OH P:TYR223 4.8 20.8 1.0 CA P:HIS120 4.9 13.5 1.0 OD2 P:ASP122 4.9 19.3 1.0 C8 P:OHN308 5.0 64.9 0.7

Cobalt binding site 3 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ X:Co301 b:15.0 occ:1.00 O X:HOH401 2.0 16.0 1.0 ND1 X:HIS120 2.0 16.7 1.0 NE2 X:HIS198 2.1 12.3 1.0 NE2 X:HIS118 2.2 13.5 1.0 O6 X:OHN305 2.3 47.9 0.7 OD2 X:ASP220 2.4 21.0 1.0 CE1 X:HIS120 3.0 17.4 1.0 CD2 X:HIS198 3.0 14.9 1.0 CD2 X:HIS118 3.0 12.4 1.0 CG X:HIS120 3.1 13.6 1.0 CE1 X:HIS198 3.1 16.7 1.0 C2 X:OHN305 3.2 47.2 0.7 CE1 X:HIS118 3.2 16.5 1.0 CG X:ASP220 3.4 17.6 1.0 CB X:HIS120 3.5 15.4 1.0 FE X:FE302 3.6 19.1 1.0 OAP X:OHN305 3.7 24.4 0.7 CB X:ASP220 3.7 16.0 1.0 NE2 X:HIS120 4.1 17.4 1.0 CD2 X:HIS123 4.1 16.3 1.0 CG X:HIS198 4.2 16.5 1.0 CD2 X:HIS120 4.2 17.4 1.0 NE2 X:HIS123 4.2 15.6 1.0 ND1 X:HIS198 4.2 16.9 1.0 CG X:HIS118 4.2 13.0 1.0 ND1 X:HIS118 4.3 15.8 1.0 OD1 X:ASP122 4.3 16.5 1.0 O9 X:OHN305 4.3 51.0 0.7 C1 X:OHN305 4.4 46.9 0.7 OD1 X:ASP220 4.5 19.6 1.0 OH X:TYR223 4.8 21.4 1.0 C8 X:OHN305 4.9 60.3 0.7 N7 X:OHN305 4.9 57.2 0.7 CA X:HIS120 5.0 13.9 1.0 OD2 X:ASP122 5.0 21.3 1.0

C.Bergonzi, M.Schwab, T.Naik, M.Elias. The Structural Determinants Accounting For the Broad Substrate Specificity of the Quorum Quenching Lactonase Gcl. Chembiochem V. 20 1848 2019.
ISSN: ESSN 1439-7633
PubMed: 30864300
DOI: 10.1002/CBIC.201900024