Iron in PDB 6n9i: Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free, PDB code: 6n9i 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)	63.93 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.420, 108.680, 78.740, 90.00, 115.84, 90.00
R / Rfree (%)	13.9 / 18.7

The structure of Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free 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 - Free (pdb code 6n9i). 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 - Free, PDB code: 6n9i:
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 - Free


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 - Free within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe313 b:35.2 occ:1.00 OD2 A:ASP220 2.0 27.7 1.0 O A:HOH422 2.1 31.3 1.0 O A:HOH525 2.2 37.6 1.0 NE2 A:HIS123 2.2 23.3 1.0 OD2 A:ASP122 2.2 29.9 1.0 NE2 A:HIS266 2.3 30.1 1.0 CG A:ASP220 2.9 24.9 1.0 CD2 A:HIS123 3.0 28.4 1.0 CG A:ASP122 3.1 32.7 1.0 OD1 A:ASP220 3.1 29.8 1.0 CD2 A:HIS266 3.2 31.4 1.0 CO A:CO301 3.3 25.0 0.7 CE1 A:HIS123 3.3 30.5 1.0 CE1 A:HIS266 3.3 29.5 1.0 OD1 A:ASP122 3.4 30.0 1.0 O A:HOH498 3.4 37.9 1.0 O A:HOH547 4.2 54.6 1.0 CG A:HIS123 4.2 24.5 1.0 NE2 A:HIS118 4.3 21.0 1.0 CB A:ASP220 4.3 22.8 1.0 CE1 A:TYR223 4.3 29.7 1.0 ND1 A:HIS123 4.3 25.3 1.0 CE1 A:HIS118 4.4 23.0 1.0 CG A:HIS266 4.4 27.8 1.0 ND1 A:HIS266 4.4 28.9 1.0 CB A:ASP122 4.5 29.7 1.0 ND1 A:HIS120 4.9 23.7 1.0

Iron binding site 2 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free


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 - Free within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe318 b:30.8 occ:1.00 OD2 B:ASP220 2.0 25.7 1.0 O B:HOH429 2.1 29.6 1.0 O B:HOH522 2.1 36.1 1.0 NE2 B:HIS123 2.2 19.2 1.0 OD2 B:ASP122 2.2 28.1 1.0 NE2 B:HIS266 2.3 25.2 1.0 CG B:ASP220 2.9 21.2 1.0 CD2 B:HIS123 3.0 20.4 1.0 CG B:ASP122 3.1 22.1 1.0 OD1 B:ASP220 3.2 23.2 1.0 CE1 B:HIS123 3.3 21.5 1.0 CE1 B:HIS266 3.3 26.6 1.0 CD2 B:HIS266 3.3 27.1 1.0 CO B:CO301 3.3 26.6 0.8 OD1 B:ASP122 3.4 27.7 1.0 O B:HOH536 3.4 32.3 1.0 CG B:HIS123 4.2 20.1 1.0 NE2 B:HIS118 4.3 17.9 1.0 CB B:ASP220 4.3 19.7 1.0 ND1 B:HIS123 4.3 23.5 1.0 O B:HOH618 4.4 57.7 1.0 CE1 B:HIS118 4.4 21.4 1.0 ND1 B:HIS266 4.4 24.5 1.0 CE1 B:TYR223 4.4 20.8 1.0 CG B:HIS266 4.5 27.8 1.0 CB B:ASP122 4.5 24.4 1.0 ND1 B:HIS120 5.0 23.7 1.0

Iron binding site 3 out of 3 in the Structure of the Quorum Quenching Lactonase From Parageobacillus Caldoxylosilyticus - Free


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 - Free within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe313 b:32.4 occ:1.00 OD2 C:ASP220 2.0 27.8 1.0 NE2 C:HIS123 2.2 22.8 1.0 O C:HOH420 2.2 34.1 1.0 OD2 C:ASP122 2.2 29.2 1.0 NE2 C:HIS266 2.3 24.5 1.0 O C:HOH564 2.3 40.1 1.0 CG C:ASP220 2.8 24.8 1.0 CD2 C:HIS123 3.0 20.2 1.0 CG C:ASP122 3.1 24.1 1.0 OD1 C:ASP220 3.1 26.4 1.0 CE1 C:HIS123 3.2 24.5 1.0 CE1 C:HIS266 3.3 30.5 1.0 CD2 C:HIS266 3.3 30.4 1.0 OD1 C:ASP122 3.4 29.9 1.0 CO C:CO301 3.4 25.9 0.7 O C:HOH535 3.4 39.8 1.0 O C:HOH597 4.2 65.0 1.0 CG C:HIS123 4.2 21.5 1.0 CB C:ASP220 4.2 23.2 1.0 NE2 C:HIS118 4.3 19.4 1.0 ND1 C:HIS123 4.3 25.3 1.0 ND1 C:HIS266 4.4 27.4 1.0 CE1 C:HIS118 4.4 22.0 1.0 CE1 C:TYR223 4.4 23.8 1.0 CB C:ASP122 4.5 27.6 1.0 CG C:HIS266 4.5 29.7 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