Cobalt in PDB 6n9i: Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free, PDB code: 6n9i 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)	63.93 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.420, 108.680, 78.740, 90.00, 115.84, 90.00
R / Rfree (%)	13.9 / 18.7

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free 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 - Free (pdb code 6n9i). 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 - Free, PDB code: 6n9i:
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 - Free


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 - Free within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:25.0 occ:0.68 O A:HOH422 1.9 31.3 1.0 ND1 A:HIS120 2.1 23.7 1.0 O A:HOH498 2.1 37.9 1.0 NE2 A:HIS118 2.2 21.0 1.0 NE2 A:HIS198 2.3 23.3 1.0 OD2 A:ASP220 2.4 27.7 1.0 CE1 A:HIS120 2.9 27.7 1.0 CD2 A:HIS118 3.1 21.1 1.0 CG A:HIS120 3.1 22.5 1.0 CD2 A:HIS198 3.2 23.5 1.0 CE1 A:HIS118 3.3 23.0 1.0 FE A:FE313 3.3 35.2 1.0 CE1 A:HIS198 3.3 26.8 1.0 CG A:ASP220 3.4 24.9 1.0 CB A:HIS120 3.6 22.4 1.0 O A:HOH525 3.6 37.6 1.0 CB A:ASP220 3.8 22.8 1.0 NE2 A:HIS123 4.1 23.3 1.0 NE2 A:HIS120 4.1 30.2 1.0 CD2 A:HIS123 4.2 28.4 1.0 CD2 A:HIS120 4.2 33.5 1.0 CG A:HIS118 4.3 20.8 1.0 ND1 A:HIS118 4.4 21.4 1.0 OH A:TYR223 4.4 27.9 1.0 CG A:HIS198 4.4 24.9 1.0 ND1 A:HIS198 4.4 28.1 1.0 OD1 A:ASP122 4.5 30.0 1.0 OD1 A:ASP220 4.6 29.8 1.0 O A:HOH547 4.6 54.6 1.0 CE1 A:TYR223 4.8 29.7 1.0 OD2 A:ASP122 4.9 29.9 1.0

Cobalt binding site 2 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free


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 - Free within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:26.6 occ:0.75 O B:HOH429 1.9 29.6 1.0 O B:HOH536 2.1 32.3 1.0 ND1 B:HIS120 2.1 23.7 1.0 NE2 B:HIS118 2.2 17.9 1.0 NE2 B:HIS198 2.3 22.0 1.0 OD2 B:ASP220 2.4 25.7 1.0 CE1 B:HIS120 3.0 24.6 1.0 CD2 B:HIS118 3.1 19.5 1.0 CD2 B:HIS198 3.2 23.4 1.0 CG B:HIS120 3.2 20.6 1.0 CE1 B:HIS118 3.3 21.4 1.0 FE B:FE318 3.3 30.8 1.0 CE1 B:HIS198 3.4 24.2 1.0 CG B:ASP220 3.4 21.2 1.0 O B:HOH522 3.5 36.1 1.0 CB B:HIS120 3.6 20.4 1.0 CB B:ASP220 3.7 19.7 1.0 NE2 B:HIS123 4.1 19.2 1.0 CD2 B:HIS123 4.2 20.4 1.0 NE2 B:HIS120 4.2 27.1 1.0 CD2 B:HIS120 4.3 27.8 1.0 CG B:HIS118 4.3 19.7 1.0 ND1 B:HIS118 4.3 21.4 1.0 CG B:HIS198 4.4 20.6 1.0 ND1 B:HIS198 4.4 23.8 1.0 OH B:TYR223 4.5 25.9 1.0 OD1 B:ASP122 4.5 27.7 1.0 OD1 B:ASP220 4.6 23.2 1.0 O B:HOH618 4.7 57.7 1.0 CE1 B:TYR223 4.9 20.8 1.0 OD2 B:ASP122 4.9 28.1 1.0

Cobalt binding site 3 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free


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 - Free within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:25.9 occ:0.68 O C:HOH420 2.0 34.1 1.0 O C:HOH535 2.1 39.8 1.0 ND1 C:HIS120 2.1 25.4 1.0 NE2 C:HIS118 2.3 19.4 1.0 NE2 C:HIS198 2.3 22.7 1.0 OD2 C:ASP220 2.4 27.8 1.0 CE1 C:HIS120 3.0 29.8 1.0 CD2 C:HIS118 3.1 19.0 1.0 CD2 C:HIS198 3.2 23.9 1.0 CG C:HIS120 3.2 20.4 1.0 CE1 C:HIS118 3.3 22.0 1.0 CE1 C:HIS198 3.4 28.9 1.0 FE C:FE313 3.4 32.4 1.0 CG C:ASP220 3.4 24.8 1.0 O C:HOH564 3.6 40.1 1.0 CB C:HIS120 3.6 22.7 1.0 CB C:ASP220 3.7 23.2 1.0 NE2 C:HIS123 4.1 22.8 1.0 NE2 C:HIS120 4.1 29.2 1.0 CD2 C:HIS123 4.2 20.2 1.0 CD2 C:HIS120 4.2 28.2 1.0 CG C:HIS118 4.3 19.1 1.0 CG C:HIS198 4.4 22.7 1.0 ND1 C:HIS118 4.4 19.0 1.0 ND1 C:HIS198 4.4 24.3 1.0 OD1 C:ASP122 4.5 29.9 1.0 OH C:TYR223 4.5 25.5 1.0 OD1 C:ASP220 4.6 26.4 1.0 O C:HOH597 4.7 65.0 1.0 CE1 C:TYR223 4.8 23.8 1.0 OD2 C:ASP122 4.9 29.2 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