Iron in PDB 6n9q: Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl, PDB code: 6n9q 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)	19.74 / 2.35
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	108.020, 108.020, 222.140, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 21.1

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Iron atom in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl (pdb code 6n9q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-Ahl, PDB code: 6n9q:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-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 Bind to Substrate C4-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe314 b:41.1 occ:1.00 OD2 P:ASP220 2.2 46.7 1.0 OD2 P:ASP122 2.2 47.7 1.0 NE2 P:HIS123 2.3 30.8 1.0 OAP P:HL4304 2.3 48.1 0.8 O P:HOH401 2.3 39.4 1.0 NE2 P:HIS266 2.3 31.3 1.0 CG P:ASP220 2.8 41.1 1.0 OD1 P:ASP220 2.9 39.8 1.0 C2 P:HL4304 2.9 74.8 0.8 CD2 P:HIS123 3.0 31.1 1.0 CG P:ASP122 3.1 42.7 1.0 CE1 P:HIS266 3.2 34.7 1.0 O6 P:HL4304 3.2 62.0 0.8 OD1 P:ASP122 3.3 38.8 1.0 CD2 P:HIS266 3.3 32.4 1.0 CE1 P:HIS123 3.4 33.9 1.0 C4 P:HL4304 3.5 57.9 0.8 CO P:CO301 3.5 37.9 1.0 C1 P:HL4304 4.0 67.5 0.8 C5 P:HL4304 4.2 60.0 0.8 CG P:HIS123 4.2 30.7 1.0 CB P:ASP220 4.3 40.2 1.0 ND1 P:HIS266 4.4 33.7 1.0 NE2 P:HIS118 4.4 30.9 1.0 ND1 P:HIS123 4.4 32.0 1.0 CG P:HIS266 4.4 34.5 1.0 CB P:ASP122 4.4 40.3 1.0 CE1 P:TYR223 4.5 39.5 1.0 CE1 P:HIS118 4.5 31.6 1.0

Iron binding site 2 out of 2 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus Bind to Substrate C4-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 Bind to Substrate C4-Ahl within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe316 b:42.5 occ:1.00 OD2 D:ASP220 2.2 44.9 1.0 OD2 D:ASP122 2.2 44.7 1.0 NE2 D:HIS123 2.3 31.1 1.0 NE2 D:HIS266 2.3 30.6 1.0 O D:HOH402 2.3 42.9 1.0 OAP D:HL4305 2.4 49.0 0.7 C2 D:HL4305 2.8 65.5 0.7 CG D:ASP220 2.9 39.7 1.0 OD1 D:ASP220 2.9 40.1 1.0 O6 D:HL4305 3.0 59.7 0.7 CD2 D:HIS123 3.0 31.6 1.0 CG D:ASP122 3.1 40.5 1.0 C4 D:HL4305 3.1 48.0 0.7 CE1 D:HIS266 3.3 33.6 1.0 CD2 D:HIS266 3.3 33.3 1.0 OD1 D:ASP122 3.3 39.7 1.0 CE1 D:HIS123 3.4 33.1 1.0 CO D:CO301 3.5 37.5 1.0 C1 D:HL4305 3.9 61.8 0.7 C5 D:HL4305 4.1 52.3 0.7 CG D:HIS123 4.2 32.6 1.0 CB D:ASP220 4.3 42.7 1.0 NE2 D:HIS118 4.3 30.0 1.0 ND1 D:HIS266 4.4 32.1 1.0 ND1 D:HIS123 4.4 33.6 1.0 CG D:HIS266 4.4 34.4 1.0 CB D:ASP122 4.5 38.6 1.0 CE1 D:HIS118 4.5 31.3 1.0 CE1 D:TYR223 4.5 35.6 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