Iron in PDB 6n9r: Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl, PDB code: 6n9r 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)	70.80 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.010, 108.590, 78.600, 90.00, 115.75, 90.00
R / Rfree (%)	17.6 / 23.5

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl also contains other interesting chemical elements:

Cobalt

(Co)

3 atoms

The binding sites of Iron atom in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl (pdb code 6n9r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl, PDB code: 6n9r:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:18.0 occ:1.00 OD2 A:ASP220 2.0 21.4 1.0 NE2 A:HIS123 2.1 12.1 1.0 OD2 A:ASP122 2.1 19.0 1.0 OAP A:OHN303 2.1 18.1 0.7 NE2 A:HIS266 2.3 17.8 1.0 O A:HOH401 2.4 20.4 1.0 CG A:ASP220 2.8 16.8 1.0 OD1 A:ASP220 2.9 18.5 1.0 C2 A:OHN303 2.9 31.9 0.7 CD2 A:HIS123 3.0 14.7 1.0 CG A:ASP122 3.0 16.9 1.0 C4 A:OHN303 3.2 21.9 0.7 CE1 A:HIS123 3.2 16.2 1.0 CD2 A:HIS266 3.2 14.3 1.0 CE1 A:HIS266 3.3 18.0 1.0 OD1 A:ASP122 3.3 16.9 1.0 O6 A:OHN303 3.5 26.1 0.7 CO A:CO301 3.6 13.7 1.0 C1 A:OHN303 3.8 32.7 0.7 C5 A:OHN303 3.9 24.9 0.7 CG A:HIS123 4.2 11.6 1.0 ND1 A:HIS123 4.2 15.4 1.0 CB A:ASP220 4.3 13.2 1.0 ND1 A:HIS266 4.4 16.9 1.0 NE2 A:HIS118 4.4 9.4 1.0 CB A:ASP122 4.4 17.4 1.0 CG A:HIS266 4.4 15.5 1.0 CE1 A:HIS118 4.5 15.2 1.0 CE1 A:TYR223 4.5 16.7 1.0 NE2 A:HIS198 5.0 12.8 1.0

Iron binding site 2 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe302 b:18.9 occ:1.00 OD2 P:ASP122 2.1 19.3 1.0 OD2 P:ASP220 2.1 21.8 1.0 NE2 P:HIS123 2.2 15.8 1.0 NE2 P:HIS266 2.3 17.1 1.0 O P:HOH402 2.3 19.9 1.0 OAP P:OHN308 2.4 24.7 0.7 CG P:ASP220 2.8 17.1 1.0 OD1 P:ASP220 2.9 18.4 1.0 CD2 P:HIS123 3.0 15.6 1.0 CG P:ASP122 3.0 19.7 1.0 C2 P:OHN308 3.1 46.7 0.7 CD2 P:HIS266 3.2 17.2 1.0 CE1 P:HIS266 3.3 16.6 1.0 CE1 P:HIS123 3.3 16.6 1.0 OD1 P:ASP122 3.3 19.0 1.0 C4 P:OHN308 3.4 34.6 0.7 O6 P:OHN308 3.6 45.7 0.7 CO P:CO301 3.6 14.0 1.0 C1 P:OHN308 3.9 41.8 0.7 C5 P:OHN308 4.0 33.1 0.7 CG P:HIS123 4.2 13.6 1.0 CB P:ASP220 4.3 15.9 1.0 ND1 P:HIS123 4.3 15.7 1.0 ND1 P:HIS266 4.4 16.7 1.0 CG P:HIS266 4.4 17.9 1.0 CB P:ASP122 4.4 19.4 1.0 NE2 P:HIS118 4.4 12.6 1.0 CE1 P:TYR223 4.5 16.7 1.0 CE1 P:HIS118 4.5 14.6 1.0

Iron binding site 3 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bound to Substrate 3-Oxo-C12-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ X:Fe302 b:19.1 occ:1.00 OAP X:OHN305 2.0 24.4 0.7 OD2 X:ASP220 2.1 21.0 1.0 OD2 X:ASP122 2.1 21.3 1.0 NE2 X:HIS123 2.2 15.6 1.0 NE2 X:HIS266 2.2 20.2 1.0 O X:HOH401 2.2 16.0 1.0 CG X:ASP220 2.8 17.6 1.0 OD1 X:ASP220 2.9 19.6 1.0 C2 X:OHN305 2.9 47.2 0.7 CD2 X:HIS123 3.0 16.3 1.0 CG X:ASP122 3.0 23.3 1.0 C4 X:OHN305 3.1 38.2 0.7 CD2 X:HIS266 3.2 19.7 1.0 CE1 X:HIS266 3.2 23.1 1.0 CE1 X:HIS123 3.3 16.2 1.0 OD1 X:ASP122 3.3 16.5 1.0 O6 X:OHN305 3.4 47.9 0.7 CO X:CO301 3.6 15.0 1.0 C1 X:OHN305 3.8 46.9 0.7 C5 X:OHN305 3.9 38.5 0.7 CG X:HIS123 4.2 15.5 1.0 CB X:ASP220 4.3 16.0 1.0 ND1 X:HIS123 4.3 17.6 1.0 ND1 X:HIS266 4.3 19.3 1.0 CG X:HIS266 4.3 19.5 1.0 CB X:ASP122 4.4 20.1 1.0 CE1 X:TYR223 4.5 17.0 1.0 NE2 X:HIS118 4.5 13.5 1.0 CE1 X:HIS118 4.6 16.5 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