Cobalt in PDB 6cgy: Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion

The structure of Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion, PDB code: 6cgy 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)	19.90 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.720, 114.740, 79.970, 90.00, 109.78, 90.00
R / Rfree (%)	17 / 19.7

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase From Alicyclobacillus Acidoterrestris Bound to A Phosphate Anion (pdb code 6cgy). 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 Phosphate Anion, PDB code: 6cgy:
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 Phosphate Anion


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 Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:17.0 occ:1.00 O1 A:PO4305 2.1 19.3 0.8 NE2 A:HIS266 2.1 17.5 1.0 OD2 A:ASP220 2.1 19.2 1.0 NE2 A:HIS123 2.1 18.2 1.0 OD2 A:ASP122 2.2 18.9 1.0 O2 A:PO4305 2.3 19.3 0.8 P A:PO4305 2.7 43.6 0.8 CG A:ASP220 2.9 17.2 1.0 OD1 A:ASP220 3.0 19.9 1.0 CD2 A:HIS123 3.0 15.4 1.0 CD2 A:HIS266 3.1 18.6 1.0 CE1 A:HIS266 3.1 18.6 1.0 CG A:ASP122 3.1 18.8 1.0 CE1 A:HIS123 3.2 20.7 1.0 OD1 A:ASP122 3.3 18.9 1.0 CO A:CO303 3.5 17.4 1.0 O3 A:PO4305 3.7 18.7 0.8 O4 A:PO4305 3.8 22.4 0.8 CG A:HIS123 4.2 17.6 1.0 ND1 A:HIS266 4.2 19.1 1.0 CG A:HIS266 4.2 16.8 1.0 ND1 A:HIS123 4.3 20.4 1.0 CB A:ASP220 4.3 16.0 1.0 NE2 A:HIS118 4.4 16.9 1.0 CE1 A:TYR223 4.5 20.1 1.0 CB A:ASP122 4.5 19.3 1.0 CE1 A:HIS118 4.5 18.0 1.0

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


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 Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Co303 b:17.4 occ:1.00 NE2 A:HIS198 2.1 16.1 1.0 O2 A:PO4305 2.2 19.3 0.8 ND1 A:HIS120 2.2 18.4 1.0 NE2 A:HIS118 2.2 16.9 1.0 OD2 A:ASP220 2.2 19.2 1.0 O3 A:PO4305 2.2 18.7 0.8 P A:PO4305 2.7 43.6 0.8 CE1 A:HIS120 3.0 21.3 1.0 CE1 A:HIS198 3.1 19.4 1.0 CD2 A:HIS118 3.1 13.5 1.0 CD2 A:HIS198 3.2 18.3 1.0 CE1 A:HIS118 3.2 18.0 1.0 CG A:HIS120 3.2 15.8 1.0 CG A:ASP220 3.3 17.2 1.0 CO A:CO302 3.5 17.0 1.0 CB A:ASP220 3.6 16.0 1.0 CB A:HIS120 3.6 16.1 1.0 O1 A:PO4305 3.6 19.3 0.8 O4 A:PO4305 3.9 22.4 0.8 ND1 A:HIS198 4.2 20.5 1.0 NE2 A:HIS120 4.2 22.3 1.0 NE2 A:HIS123 4.2 18.2 1.0 CD2 A:HIS123 4.2 15.4 1.0 CG A:HIS198 4.3 19.0 1.0 CG A:HIS118 4.3 15.1 1.0 ND1 A:HIS118 4.3 15.8 1.0 CD2 A:HIS120 4.3 20.6 1.0 OD1 A:ASP220 4.4 19.9 1.0 OD1 A:ASP122 4.5 18.9 1.0 OH A:TYR223 4.6 22.7 1.0 CE1 A:TYR223 4.8 20.1 1.0

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


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 Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ H:Co302 b:18.9 occ:1.00 NE2 H:HIS123 2.1 19.0 1.0 NE2 H:HIS266 2.1 18.8 1.0 O3 H:PO4306 2.1 18.9 0.7 OD2 H:ASP220 2.2 19.8 1.0 OD2 H:ASP122 2.2 21.7 1.0 O2 H:PO4306 2.3 18.0 0.7 P H:PO4306 2.7 36.4 0.7 CG H:ASP220 2.9 17.5 1.0 OD1 H:ASP220 3.0 20.1 1.0 CD2 H:HIS123 3.0 17.4 1.0 CE1 H:HIS266 3.1 20.6 1.0 CD2 H:HIS266 3.1 18.6 1.0 CG H:ASP122 3.1 21.7 1.0 CE1 H:HIS123 3.1 17.8 1.0 OD1 H:ASP122 3.4 21.4 1.0 CO H:CO303 3.6 18.8 1.0 O1 H:PO4306 3.7 18.1 0.7 O4 H:PO4306 3.9 22.6 0.7 CG H:HIS123 4.2 16.8 1.0 ND1 H:HIS266 4.2 19.1 1.0 ND1 H:HIS123 4.2 20.4 1.0 CG H:HIS266 4.2 19.6 1.0 CB H:ASP220 4.4 18.3 1.0 NE2 H:HIS118 4.4 17.0 1.0 CE1 H:TYR223 4.4 19.6 1.0 CE1 H:HIS118 4.5 16.4 1.0 CB H:ASP122 4.5 21.3 1.0

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


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 Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ H:Co303 b:18.8 occ:1.00 NE2 H:HIS198 2.1 17.5 1.0 ND1 H:HIS120 2.2 19.2 1.0 O2 H:PO4306 2.2 18.0 0.7 OD2 H:ASP220 2.2 19.8 1.0 NE2 H:HIS118 2.2 17.0 1.0 O1 H:PO4306 2.2 18.1 0.7 P H:PO4306 2.7 36.4 0.7 CE1 H:HIS120 3.0 21.2 1.0 CD2 H:HIS118 3.1 17.1 1.0 CE1 H:HIS198 3.1 19.8 1.0 CD2 H:HIS198 3.1 19.3 1.0 CG H:ASP220 3.2 17.5 1.0 CG H:HIS120 3.2 16.9 1.0 CE1 H:HIS118 3.2 16.4 1.0 CO H:CO302 3.6 18.9 1.0 CB H:ASP220 3.6 18.3 1.0 CB H:HIS120 3.6 17.0 1.0 O3 H:PO4306 3.7 18.9 0.7 O4 H:PO4306 3.9 22.6 0.7 NE2 H:HIS123 4.1 19.0 1.0 NE2 H:HIS120 4.2 20.9 1.0 ND1 H:HIS198 4.2 21.7 1.0 CD2 H:HIS123 4.2 17.4 1.0 CG H:HIS118 4.3 17.7 1.0 CG H:HIS198 4.3 18.5 1.0 CD2 H:HIS120 4.3 20.5 1.0 ND1 H:HIS118 4.3 17.7 1.0 OD1 H:ASP220 4.4 20.1 1.0 OD1 H:ASP122 4.5 21.4 1.0 OH H:TYR223 4.5 24.0 1.0 CE1 H:TYR223 4.8 19.6 1.0

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


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 Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ L:Co301 b:20.2 occ:1.00 O1 L:PO4304 1.9 22.0 0.8 NE2 L:HIS123 2.1 21.1 1.0 NE2 L:HIS266 2.1 20.6 1.0 OD2 L:ASP220 2.2 20.1 1.0 OD2 L:ASP122 2.2 23.6 1.0 O3 L:PO4304 2.2 19.8 0.8 P L:PO4304 2.7 46.7 0.8 CG L:ASP220 2.9 19.8 1.0 OD1 L:ASP220 2.9 20.2 1.0 CD2 L:HIS123 3.0 21.1 1.0 CE1 L:HIS266 3.0 24.7 1.0 CE1 L:HIS123 3.1 18.1 1.0 CG L:ASP122 3.1 29.5 1.0 CD2 L:HIS266 3.1 22.2 1.0 OD1 L:ASP122 3.3 22.8 1.0 CO L:CO302 3.5 19.5 1.0 O2 L:PO4304 3.7 23.4 0.8 O4 L:PO4304 3.8 25.4 0.8 CG L:HIS123 4.2 18.9 1.0 ND1 L:HIS123 4.2 22.6 1.0 ND1 L:HIS266 4.2 21.6 1.0 CG L:HIS266 4.3 22.0 1.0 CB L:ASP220 4.3 18.5 1.0 CE1 L:TYR223 4.4 18.8 1.0 NE2 L:HIS118 4.4 21.5 1.0 CE1 L:HIS118 4.5 19.6 1.0 CB L:ASP122 4.5 22.8 1.0

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


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 Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ L:Co302 b:19.5 occ:1.00 OD2 L:ASP220 2.2 20.1 1.0 ND1 L:HIS120 2.2 20.2 1.0 NE2 L:HIS118 2.2 21.5 1.0 NE2 L:HIS198 2.2 17.9 1.0 O2 L:PO4304 2.2 23.4 0.8 O3 L:PO4304 2.2 19.8 0.8 P L:PO4304 2.7 46.7 0.8 CE1 L:HIS120 3.0 20.4 1.0 CD2 L:HIS118 3.1 18.2 1.0 CD2 L:HIS198 3.1 22.2 1.0 CE1 L:HIS198 3.2 22.8 1.0 CE1 L:HIS118 3.2 19.6 1.0 CG L:ASP220 3.2 19.8 1.0 CG L:HIS120 3.2 20.2 1.0 CO L:CO301 3.5 20.2 1.0 O1 L:PO4304 3.6 22.0 0.8 CB L:ASP220 3.6 18.5 1.0 CB L:HIS120 3.6 20.4 1.0 O4 L:PO4304 4.0 25.4 0.8 NE2 L:HIS123 4.1 21.1 1.0 NE2 L:HIS120 4.2 22.8 1.0 CD2 L:HIS123 4.2 21.1 1.0 ND1 L:HIS198 4.3 20.4 1.0 CG L:HIS198 4.3 19.9 1.0 CG L:HIS118 4.3 17.9 1.0 ND1 L:HIS118 4.3 19.7 1.0 CD2 L:HIS120 4.3 23.0 1.0 OD1 L:ASP220 4.3 20.2 1.0 OD1 L:ASP122 4.5 22.8 1.0 OH L:TYR223 4.5 23.3 1.0 CE1 L:TYR223 4.7 18.8 1.0 O L:HOH470 4.9 43.6 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