Cobalt in PDB 6cgz: Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-Ahl

The structure of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-Ahl, PDB code: 6cgz 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)	57.31 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.940, 88.690, 97.680, 90.00, 128.24, 90.00
R / Rfree (%)	16.3 / 19.2

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-Ahl (pdb code 6cgz). 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 C6-Ahl, PDB code: 6cgz:
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 C6-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 Alicyclobacillus Acidoterrestris Bound to C6-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:18.7 occ:1.00 O2 A:HL6307 2.1 19.2 0.6 NE2 A:HIS266 2.1 19.5 1.0 OD2 A:ASP122 2.1 22.0 1.0 NE2 A:HIS123 2.2 19.1 1.0 OD1 A:ASP220 2.3 21.6 1.0 OD2 A:ASP220 2.3 19.1 1.0 CG A:ASP220 2.6 18.5 1.0 C1 A:HL6307 2.9 27.9 0.6 C2 A:HL6307 3.0 20.5 0.6 CD2 A:HIS123 3.0 18.3 1.0 CE1 A:HIS266 3.1 20.0 1.0 CD2 A:HIS266 3.1 19.4 1.0 CG A:ASP122 3.1 20.2 1.0 O1 A:HL6307 3.2 24.2 0.6 CE1 A:HIS123 3.2 21.8 1.0 OD1 A:ASP122 3.5 19.4 1.0 CO A:CO302 4.0 19.2 1.0 C4 A:HL6307 4.1 28.1 0.6 CB A:ASP220 4.2 18.5 1.0 ND1 A:HIS266 4.2 19.6 1.0 CG A:HIS123 4.2 18.4 1.0 C3 A:HL6307 4.2 24.5 0.6 CG A:HIS266 4.2 19.1 1.0 ND1 A:HIS123 4.3 21.2 1.0 CB A:ASP122 4.4 19.9 1.0 CE1 A:TYR223 4.5 20.9 1.0 CE1 A:HIS118 4.7 17.3 1.0 NE2 A:HIS118 4.8 17.8 1.0

Cobalt binding site 2 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-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 Alicyclobacillus Acidoterrestris Bound to C6-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:19.2 occ:1.00 OD2 A:ASP220 2.0 19.1 1.0 O1 A:HL6307 2.1 24.2 0.6 ND1 A:HIS120 2.1 20.5 1.0 NE2 A:HIS118 2.1 17.8 1.0 NE2 A:HIS198 2.2 18.8 1.0 CE1 A:HIS120 3.0 23.8 1.0 CD2 A:HIS198 3.0 19.1 1.0 CD2 A:HIS118 3.0 17.0 1.0 CG A:HIS120 3.1 20.3 1.0 C1 A:HL6307 3.1 27.9 0.6 CG A:ASP220 3.1 18.5 1.0 CE1 A:HIS118 3.1 17.3 1.0 CE1 A:HIS198 3.3 19.5 1.0 CB A:HIS120 3.5 18.3 1.0 CB A:ASP220 3.6 18.5 1.0 O2 A:HL6307 3.8 19.2 0.6 CO A:CO301 4.0 18.7 1.0 O3 A:HL6307 4.0 32.0 0.6 C5 A:HL6307 4.1 35.0 0.6 NE2 A:HIS120 4.2 22.7 1.0 N A:HL6307 4.2 35.2 0.6 C4 A:HL6307 4.2 28.1 0.6 CD2 A:HIS123 4.2 18.3 1.0 CD2 A:HIS120 4.2 22.8 1.0 CG A:HIS118 4.2 16.1 1.0 ND1 A:HIS118 4.2 16.6 1.0 CG A:HIS198 4.2 18.2 1.0 OD1 A:ASP122 4.2 19.4 1.0 OD1 A:ASP220 4.2 21.6 1.0 ND1 A:HIS198 4.3 19.6 1.0 NE2 A:HIS123 4.5 19.1 1.0 C6 A:HL6307 4.8 35.7 0.6 CA A:HIS120 4.9 17.2 1.0 OD2 A:ASP122 5.0 22.0 1.0

Cobalt binding site 3 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-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 Alicyclobacillus Acidoterrestris Bound to C6-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:20.2 occ:1.00 O B:HOH402 1.4 43.0 1.0 NE2 B:HIS266 2.0 19.9 1.0 NE2 B:HIS123 2.1 20.0 1.0 O2 B:HL6305 2.1 23.9 0.7 OD2 B:ASP122 2.2 21.6 1.0 OD1 B:ASP220 2.2 20.6 1.0 OD2 B:ASP220 2.4 19.2 1.0 CG B:ASP220 2.6 18.0 1.0 C2 B:HL6305 3.0 26.9 0.7 CD2 B:HIS266 3.0 20.6 1.0 CE1 B:HIS266 3.0 20.1 1.0 CD2 B:HIS123 3.0 20.0 1.0 C1 B:HL6305 3.1 34.8 0.7 CG B:ASP122 3.1 22.4 1.0 CE1 B:HIS123 3.2 22.6 1.0 O1 B:HL6305 3.4 30.4 0.7 OD1 B:ASP122 3.5 20.6 1.0 CO B:CO302 3.9 18.8 1.0 ND1 B:HIS266 4.1 20.0 1.0 CB B:ASP220 4.1 18.5 1.0 CG B:HIS266 4.2 21.6 1.0 CG B:HIS123 4.2 20.0 1.0 ND1 B:HIS123 4.3 22.2 1.0 C4 B:HL6305 4.3 33.3 0.7 C3 B:HL6305 4.3 31.2 0.7 CE1 B:TYR223 4.4 21.2 1.0 CB B:ASP122 4.5 20.4 1.0 CE1 B:HIS118 4.6 18.8 1.0 NE2 B:HIS118 4.7 18.0 1.0 CA B:ASP220 4.9 18.1 1.0

Cobalt binding site 4 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-Ahl


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 C6-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:18.8 occ:1.00 OD2 B:ASP220 2.0 19.2 1.0 ND1 B:HIS120 2.1 20.6 1.0 NE2 B:HIS118 2.1 18.0 1.0 NE2 B:HIS198 2.2 19.0 1.0 O1 B:HL6305 2.2 30.4 0.7 CE1 B:HIS120 3.0 20.8 1.0 CD2 B:HIS118 3.0 18.1 1.0 CD2 B:HIS198 3.0 19.5 1.0 O B:HOH402 3.1 43.0 1.0 CG B:ASP220 3.1 18.0 1.0 CG B:HIS120 3.1 20.5 1.0 CE1 B:HIS118 3.1 18.8 1.0 CE1 B:HIS198 3.2 20.8 1.0 C1 B:HL6305 3.2 34.8 0.7 CB B:HIS120 3.5 19.1 1.0 CB B:ASP220 3.6 18.5 1.0 O2 B:HL6305 3.8 23.9 0.7 CO B:CO301 3.9 20.2 1.0 NE2 B:HIS120 4.1 21.9 1.0 OD1 B:ASP220 4.2 20.6 1.0 CG B:HIS118 4.2 17.9 1.0 ND1 B:HIS118 4.2 18.4 1.0 CD2 B:HIS120 4.2 21.6 1.0 CG B:HIS198 4.2 18.8 1.0 ND1 B:HIS198 4.2 19.1 1.0 CD2 B:HIS123 4.3 20.0 1.0 OD1 B:ASP122 4.3 20.6 1.0 O3 B:HL6305 4.4 41.9 0.7 C5 B:HL6305 4.4 41.1 0.7 N B:HL6305 4.4 43.1 0.7 C4 B:HL6305 4.4 33.3 0.7 NE2 B:HIS123 4.5 20.0 1.0 OH B:TYR223 4.9 25.8 1.0 C6 B:HL6305 4.9 42.1 0.7 CA B:HIS120 5.0 18.8 1.0

Cobalt binding site 5 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-Ahl


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 C6-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:21.2 occ:1.00 NE2 C:HIS266 2.1 22.5 1.0 NE2 C:HIS123 2.1 20.7 1.0 O2 C:HL6304 2.1 25.0 0.7 OD2 C:ASP122 2.1 22.8 1.0 OD1 C:ASP220 2.3 20.1 1.0 OD2 C:ASP220 2.4 20.7 1.0 CG C:ASP220 2.6 19.9 1.0 CD2 C:HIS123 3.0 19.9 1.0 CD2 C:HIS266 3.0 22.6 1.0 C2 C:HL6304 3.0 26.3 0.7 O C:HOH401 3.0 41.4 1.0 CG C:ASP122 3.1 22.5 1.0 CE1 C:HIS266 3.1 22.7 1.0 CE1 C:HIS123 3.2 21.0 1.0 C1 C:HL6304 3.2 31.7 0.7 OD1 C:ASP122 3.4 21.0 1.0 O1 C:HL6304 3.7 33.9 0.7 CO C:CO302 3.9 21.1 1.0 CB C:ASP220 4.1 19.0 1.0 CG C:HIS123 4.2 20.1 1.0 CG C:HIS266 4.2 24.3 1.0 ND1 C:HIS266 4.2 23.5 1.0 C4 C:HL6304 4.2 31.8 0.7 ND1 C:HIS123 4.2 22.0 1.0 C3 C:HL6304 4.3 30.0 0.7 CB C:ASP122 4.4 21.8 1.0 CE1 C:TYR223 4.4 22.6 1.0 CE1 C:HIS118 4.7 20.5 1.0 NE2 C:HIS118 4.8 20.2 1.0 CA C:ASP220 4.9 20.0 1.0 CD1 C:TYR223 5.0 22.2 1.0

Cobalt binding site 6 out of 6 in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to C6-Ahl


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 C6-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ C:Co302 b:21.1 occ:1.00 OD2 C:ASP220 1.9 20.7 1.0 ND1 C:HIS120 2.1 24.4 1.0 NE2 C:HIS118 2.1 20.2 1.0 O C:HOH401 2.1 41.4 1.0 NE2 C:HIS198 2.1 20.4 1.0 O1 C:HL6304 2.7 33.9 0.7 CE1 C:HIS120 3.0 26.3 1.0 CD2 C:HIS118 3.0 20.1 1.0 CG C:ASP220 3.0 19.9 1.0 CD2 C:HIS198 3.1 20.4 1.0 CG C:HIS120 3.1 23.8 1.0 CE1 C:HIS198 3.1 20.6 1.0 CE1 C:HIS118 3.2 20.5 1.0 CB C:HIS120 3.5 21.6 1.0 CB C:ASP220 3.5 19.0 1.0 C1 C:HL6304 3.6 31.7 0.7 CO C:CO301 3.9 21.2 1.0 O2 C:HL6304 4.0 25.0 0.7 NE2 C:HIS120 4.1 26.9 1.0 O3 C:HL6304 4.1 39.6 0.7 OD1 C:ASP220 4.1 20.1 1.0 CG C:HIS118 4.2 20.4 1.0 CD2 C:HIS120 4.2 25.2 1.0 CD2 C:HIS123 4.2 19.9 1.0 ND1 C:HIS198 4.2 20.5 1.0 CG C:HIS198 4.2 19.4 1.0 ND1 C:HIS118 4.2 21.0 1.0 OD1 C:ASP122 4.3 21.0 1.0 NE2 C:HIS123 4.5 20.7 1.0 C4 C:HL6304 4.7 31.8 0.7 CA C:HIS120 4.9 20.4 1.0 OH C:TYR223 5.0 23.5 1.0 C5 C:HL6304 5.0 41.7 0.7

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