Cobalt in PDB 6ch0: Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule

The structure of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule, PDB code: 6ch0 was solved by C.Bergonzi, M.Schwab, T.Naik, D.Daude, E.Chabriere, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.83 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.840, 113.500, 79.100, 90.00, 108.91, 90.00
R / Rfree (%)	18.5 / 22.9

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule (pdb code 6ch0). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule, PDB code: 6ch0:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule


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 Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:31.9 occ:1.00 O2 C:GOL306 1.9 35.6 1.0 OD2 C:ASP122 2.0 35.7 1.0 NE2 C:HIS123 2.1 26.5 1.0 NE2 C:HIS266 2.2 28.8 1.0 OD1 C:ASP220 2.4 28.5 1.0 OD2 C:ASP220 2.5 29.2 1.0 CG C:ASP220 2.8 34.7 1.0 CD2 C:HIS123 2.9 29.8 1.0 CG C:ASP122 3.1 39.6 1.0 CD2 C:HIS266 3.1 29.9 1.0 C2 C:GOL306 3.2 48.3 1.0 CE1 C:HIS266 3.2 28.1 1.0 CE1 C:HIS123 3.2 34.8 1.0 O3 C:GOL306 3.2 55.3 1.0 OD1 C:ASP122 3.5 40.2 1.0 C3 C:GOL306 3.6 52.6 1.0 CO C:CO302 3.9 30.0 1.0 C1 C:GOL306 4.0 50.9 1.0 CG C:HIS123 4.1 32.6 1.0 ND1 C:HIS123 4.2 35.6 1.0 ND1 C:HIS266 4.3 31.3 1.0 CG C:HIS266 4.3 32.9 1.0 CB C:ASP220 4.3 34.3 1.0 CB C:ASP122 4.3 39.4 1.0 CE1 C:TYR223 4.6 36.8 1.0 CE1 C:HIS118 4.6 27.2 1.0 NE2 C:HIS118 4.7 24.3 1.0

Cobalt binding site 2 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule


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 Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule within 5.0Å range: probe atom residue distance (Å) B Occ C:Co302 b:30.0 occ:1.00 OD2 C:ASP220 1.9 29.2 1.0 O3 C:GOL306 1.9 55.3 1.0 ND1 C:HIS120 2.1 27.3 1.0 NE2 C:HIS118 2.1 24.3 1.0 NE2 C:HIS198 2.2 31.0 1.0 C3 C:GOL306 2.8 52.6 1.0 CD2 C:HIS118 3.0 25.8 1.0 CE1 C:HIS120 3.0 31.2 1.0 CG C:ASP220 3.0 34.7 1.0 CE1 C:HIS198 3.1 27.2 1.0 CG C:HIS120 3.1 27.6 1.0 CE1 C:HIS118 3.2 27.2 1.0 CD2 C:HIS198 3.2 31.0 1.0 CB C:HIS120 3.5 28.8 1.0 CB C:ASP220 3.6 34.3 1.0 CO C:CO301 3.9 31.9 1.0 C2 C:GOL306 4.0 48.3 1.0 OD1 C:ASP220 4.1 28.5 1.0 NE2 C:HIS120 4.1 29.4 1.0 O2 C:GOL306 4.2 35.6 1.0 CG C:HIS118 4.2 24.7 1.0 ND1 C:HIS118 4.2 28.4 1.0 CD2 C:HIS120 4.2 28.7 1.0 ND1 C:HIS198 4.3 29.1 1.0 CD2 C:HIS123 4.3 29.8 1.0 CG C:HIS198 4.3 27.6 1.0 OD1 C:ASP122 4.4 40.2 1.0 NE2 C:HIS123 4.5 26.5 1.0 OD2 C:ASP122 4.9 35.7 1.0 CA C:HIS120 5.0 29.4 1.0 OH C:TYR223 5.0 34.9 1.0

Cobalt binding site 3 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule


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 Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule within 5.0Å range: probe atom residue distance (Å) B Occ F:Co301 b:36.7 occ:1.00 O2 F:GOL305 1.9 57.5 1.0 NE2 F:HIS123 2.1 36.7 1.0 NE2 F:HIS266 2.1 30.3 1.0 OD2 F:ASP122 2.2 39.0 1.0 OD1 F:ASP220 2.4 32.2 1.0 OD2 F:ASP220 2.6 31.7 1.0 C2 F:GOL305 2.6 61.7 1.0 CG F:ASP220 2.8 36.5 1.0 CD2 F:HIS123 2.9 33.9 1.0 CE1 F:HIS266 3.1 32.4 1.0 CG F:ASP122 3.1 38.1 1.0 CD2 F:HIS266 3.2 31.7 1.0 C1 F:GOL305 3.2 71.8 1.0 O1 F:GOL305 3.2 61.1 1.0 CE1 F:HIS123 3.2 37.0 1.0 OD1 F:ASP122 3.4 40.8 1.0 CO F:CO302 3.9 35.5 1.0 C3 F:GOL305 4.0 54.6 1.0 CG F:HIS123 4.1 33.9 1.0 ND1 F:HIS266 4.2 30.7 1.0 ND1 F:HIS123 4.2 39.3 1.0 CB F:ASP220 4.3 31.5 1.0 CG F:HIS266 4.3 29.8 1.0 CB F:ASP122 4.5 41.7 1.0 NE2 F:HIS118 4.6 38.4 1.0 CE1 F:HIS118 4.6 35.9 1.0 CE1 F:TYR223 4.6 40.8 1.0 O3 F:GOL305 5.0 62.9 1.0

Cobalt binding site 4 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule within 5.0Å range: probe atom residue distance (Å) B Occ F:Co302 b:35.5 occ:1.00 OD2 F:ASP220 2.0 31.7 1.0 ND1 F:HIS120 2.0 33.6 1.0 O1 F:GOL305 2.0 61.1 1.0 NE2 F:HIS118 2.1 38.4 1.0 NE2 F:HIS198 2.2 36.9 1.0 C1 F:GOL305 2.7 71.8 1.0 CE1 F:HIS120 2.9 38.6 1.0 CD2 F:HIS118 3.0 35.1 1.0 CG F:HIS120 3.0 32.6 1.0 CD2 F:HIS198 3.1 36.8 1.0 CG F:ASP220 3.1 36.5 1.0 CE1 F:HIS198 3.2 40.6 1.0 CE1 F:HIS118 3.2 35.9 1.0 CB F:HIS120 3.4 33.8 1.0 CB F:ASP220 3.7 31.5 1.0 CO F:CO301 3.9 36.7 1.0 C2 F:GOL305 3.9 61.7 1.0 NE2 F:HIS120 4.0 36.9 1.0 CD2 F:HIS120 4.1 36.6 1.0 CG F:HIS118 4.2 34.4 1.0 OD1 F:ASP220 4.2 32.2 1.0 CD2 F:HIS123 4.2 33.9 1.0 CG F:HIS198 4.2 34.0 1.0 O2 F:GOL305 4.3 57.5 1.0 ND1 F:HIS118 4.3 37.6 1.0 ND1 F:HIS198 4.3 39.8 1.0 OD1 F:ASP122 4.3 40.8 1.0 NE2 F:HIS123 4.5 36.7 1.0 CA F:HIS120 4.9 33.4 1.0

Cobalt binding site 5 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule within 5.0Å range: probe atom residue distance (Å) B Occ I:Co301 b:37.0 occ:1.00 O2 I:GOL305 1.8 47.6 1.0 NE2 I:HIS123 2.1 33.3 1.0 NE2 I:HIS266 2.1 44.2 1.0 OD2 I:ASP122 2.3 47.7 1.0 OD1 I:ASP220 2.4 36.8 1.0 OD2 I:ASP220 2.4 35.6 1.0 C2 I:GOL305 2.6 61.9 1.0 CG I:ASP220 2.7 36.8 1.0 CD2 I:HIS123 2.9 42.3 1.0 CE1 I:HIS266 3.0 41.2 1.0 C3 I:GOL305 3.1 67.2 1.0 O3 I:GOL305 3.1 59.1 1.0 CE1 I:HIS123 3.2 39.0 1.0 CD2 I:HIS266 3.2 46.5 1.0 CG I:ASP122 3.2 48.6 1.0 OD1 I:ASP122 3.4 51.3 1.0 CO I:CO302 3.8 36.5 1.0 C1 I:GOL305 4.0 63.2 1.0 CG I:HIS123 4.1 36.1 1.0 ND1 I:HIS266 4.1 44.1 1.0 ND1 I:HIS123 4.2 38.9 1.0 CB I:ASP220 4.2 37.3 1.0 CG I:HIS266 4.3 46.8 1.0 CE1 I:TYR223 4.5 39.8 1.0 CE1 I:HIS118 4.5 33.8 1.0 CB I:ASP122 4.6 49.0 1.0 NE2 I:HIS118 4.6 27.7 1.0 O1 I:GOL305 4.9 61.6 1.0

Cobalt binding site 6 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Glycerol Molecule within 5.0Å range: probe atom residue distance (Å) B Occ I:Co302 b:36.5 occ:1.00 O3 I:GOL305 1.6 59.1 1.0 OD2 I:ASP220 1.9 35.6 1.0 NE2 I:HIS118 2.0 27.7 1.0 NE2 I:HIS198 2.2 38.5 1.0 ND1 I:HIS120 2.2 36.4 1.0 C3 I:GOL305 2.7 67.2 1.0 CD2 I:HIS118 2.9 32.4 1.0 CD2 I:HIS198 2.9 31.6 1.0 CG I:ASP220 3.0 36.8 1.0 CE1 I:HIS118 3.1 33.8 1.0 CE1 I:HIS120 3.1 39.6 1.0 CG I:HIS120 3.2 40.8 1.0 CE1 I:HIS198 3.3 34.9 1.0 CB I:ASP220 3.5 37.3 1.0 CB I:HIS120 3.5 36.3 1.0 CO I:CO301 3.8 37.0 1.0 C2 I:GOL305 3.9 61.9 1.0 OD1 I:ASP220 4.0 36.8 1.0 CG I:HIS118 4.1 28.1 1.0 ND1 I:HIS118 4.1 30.7 1.0 CD2 I:HIS123 4.2 42.3 1.0 CG I:HIS198 4.2 29.8 1.0 NE2 I:HIS120 4.3 44.0 1.0 CD2 I:HIS120 4.3 37.5 1.0 ND1 I:HIS198 4.3 36.7 1.0 O2 I:GOL305 4.4 47.6 1.0 NE2 I:HIS123 4.4 33.3 1.0 OD1 I:ASP122 4.5 51.3 1.0 OH I:TYR223 4.8 42.5 1.0 CA I:HIS120 5.0 35.8 1.0

C.Bergonzi, M.Schwab, T.Naik, D.Daude, E.Chabriere, M.Elias. Structural and Biochemical Characterization of Aal, A Quorum Quenching Lactonase with Unusual Kinetic Properties. Sci Rep V. 8 11262 2018.
ISSN: ESSN 2045-2322
PubMed: 30050039
DOI: 10.1038/S41598-018-28988-5