Cobalt in PDB 6n9q: Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl, PDB code: 6n9q 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)	19.74 / 2.35
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	108.020, 108.020, 222.140, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 21.1

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl (pdb code 6n9q). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl, PDB code: 6n9q:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-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 Bind to Substrate C4-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ P:Co301 b:37.9 occ:1.00 O P:HOH401 2.1 39.4 1.0 ND1 P:HIS120 2.1 30.9 1.0 NE2 P:HIS198 2.1 34.9 1.0 NE2 P:HIS118 2.2 30.9 1.0 OD2 P:ASP220 2.2 46.7 1.0 O6 P:HL4304 2.6 62.0 0.8 CE1 P:HIS120 3.0 32.9 1.0 CD2 P:HIS118 3.0 29.6 1.0 CD2 P:HIS198 3.1 35.6 1.0 CG P:HIS120 3.1 27.2 1.0 CE1 P:HIS198 3.2 38.3 1.0 CE1 P:HIS118 3.3 31.6 1.0 CG P:ASP220 3.3 41.1 1.0 CB P:HIS120 3.5 31.8 1.0 FE P:FE314 3.5 41.1 1.0 C2 P:HL4304 3.6 74.8 0.8 CB P:ASP220 3.7 40.2 1.0 NE2 P:HIS120 4.1 35.1 1.0 CD2 P:HIS123 4.2 31.1 1.0 OAP P:HL4304 4.2 48.1 0.8 CG P:HIS118 4.2 29.9 1.0 CD2 P:HIS120 4.2 33.4 1.0 CG P:HIS198 4.2 36.5 1.0 ND1 P:HIS198 4.2 39.3 1.0 NE2 P:HIS123 4.2 30.8 1.0 ND1 P:HIS118 4.3 33.1 1.0 OD1 P:ASP220 4.4 39.8 1.0 OD1 P:ASP122 4.4 38.8 1.0 O9 P:HL4304 4.5 73.8 0.8 C1 P:HL4304 4.6 67.5 0.8 OH P:TYR223 4.6 36.7 1.0 CA P:HIS120 5.0 32.3 1.0

Cobalt binding site 2 out of 2 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-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 Bind to Substrate C4-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:37.5 occ:1.00 ND1 D:HIS120 2.1 31.9 1.0 O D:HOH402 2.1 42.9 1.0 NE2 D:HIS118 2.1 30.0 1.0 NE2 D:HIS198 2.2 32.8 1.0 OD2 D:ASP220 2.2 44.9 1.0 O6 D:HL4305 2.2 59.7 0.7 CD2 D:HIS118 3.0 30.9 1.0 CE1 D:HIS120 3.0 33.2 1.0 CD2 D:HIS198 3.1 35.9 1.0 CG D:HIS120 3.1 28.5 1.0 CE1 D:HIS198 3.2 40.9 1.0 CE1 D:HIS118 3.2 31.3 1.0 CG D:ASP220 3.3 39.7 1.0 C2 D:HL4305 3.4 65.5 0.7 CB D:HIS120 3.5 32.3 1.0 FE D:FE316 3.5 42.5 1.0 CB D:ASP220 3.7 42.7 1.0 OAP D:HL4305 4.1 49.0 0.7 NE2 D:HIS120 4.1 34.1 1.0 CD2 D:HIS123 4.2 31.6 1.0 CG D:HIS118 4.2 32.2 1.0 CD2 D:HIS120 4.2 33.3 1.0 ND1 D:HIS198 4.2 37.4 1.0 CG D:HIS198 4.3 39.0 1.0 ND1 D:HIS118 4.3 34.0 1.0 NE2 D:HIS123 4.3 31.1 1.0 OD1 D:ASP220 4.4 40.1 1.0 OD1 D:ASP122 4.4 39.7 1.0 C1 D:HL4305 4.5 61.8 0.7 O9 D:HL4305 4.6 74.1 0.7 OH D:TYR223 4.7 40.3 1.0 N7 D:HL4305 4.9 73.1 0.7 CA D:HIS120 5.0 32.7 1.0 C8 D:HL4305 5.0 72.0 0.7

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