Iron in PDB 9ayt: Structure of the Quorum Quenching Lactonase Gcl Bound to N-Hexanoyl-L- Homoserine Lactone

The structure of Structure of the Quorum Quenching Lactonase Gcl Bound to N-Hexanoyl-L- Homoserine Lactone, PDB code: 9ayt was solved by M.Corbella, J.A.Bravo, A.O.Demkiv, A.R.Calixto, K.Sompiyachoke, C.Bergonzi, S.C.L.Kamerlin, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.17 / 2.10
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	108.5, 108.5, 228.5, 90, 90, 120
R / Rfree (%)	19.2 / 22

The structure of Structure of the Quorum Quenching Lactonase Gcl Bound to N-Hexanoyl-L- Homoserine Lactone also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Iron atom in the Structure of the Quorum Quenching Lactonase Gcl Bound to N-Hexanoyl-L- Homoserine Lactone (pdb code 9ayt). 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 Gcl Bound to N-Hexanoyl-L- Homoserine Lactone, PDB code: 9ayt:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of the Quorum Quenching Lactonase Gcl Bound to N-Hexanoyl-L- Homoserine Lactone


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 Gcl Bound to N-Hexanoyl-L- Homoserine Lactone within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe302 b:39.6 occ:1.00 OD2 P:ASP220 2.1 40.3 1.0 OD2 P:ASP122 2.1 38.5 1.0 NE2 P:HIS123 2.2 33.9 1.0 O2 P:HL6315 2.2 39.6 0.8 O P:HOH410 2.2 41.8 1.0 NE2 P:HIS266 2.3 32.6 1.0 CG P:ASP220 2.8 40.3 1.0 OD1 P:ASP220 2.9 41.8 1.0 C2 P:HL6315 2.9 41.3 0.8 CD2 P:HIS123 3.0 36.9 1.0 C1 P:HL6315 3.1 64.9 0.8 CG P:ASP122 3.1 41.3 1.0 CE1 P:HIS266 3.2 35.9 1.0 CE1 P:HIS123 3.3 35.1 1.0 CD2 P:HIS266 3.3 35.6 1.0 OD1 P:ASP122 3.5 40.5 1.0 CO P:CO301 3.6 43.9 1.0 O1 P:HL6315 3.7 49.9 0.8 C4 P:HL6315 3.9 65.0 0.8 C3 P:HL6315 4.0 48.3 0.8 CG P:HIS123 4.2 35.1 1.0 CB P:ASP220 4.3 34.6 1.0 ND1 P:HIS123 4.3 33.1 1.0 ND1 P:HIS266 4.4 34.0 1.0 NE2 P:HIS118 4.4 33.2 1.0 CG P:HIS266 4.4 37.4 1.0 CB P:ASP122 4.5 36.9 1.0 CE1 P:TYR223 4.5 36.9 1.0 CE1 P:HIS118 4.5 35.5 1.0

Iron binding site 2 out of 2 in the Structure of the Quorum Quenching Lactonase Gcl Bound to N-Hexanoyl-L- Homoserine Lactone


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 Gcl Bound to N-Hexanoyl-L- Homoserine Lactone within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe302 b:39.8 occ:1.00 O2 D:HL6318 2.0 42.1 0.8 OD2 D:ASP122 2.1 37.3 1.0 OD2 D:ASP220 2.2 41.2 1.0 NE2 D:HIS123 2.2 34.7 1.0 NE2 D:HIS266 2.3 30.4 1.0 O D:HOH401 2.3 42.6 1.0 C2 D:HL6318 2.6 44.8 0.8 CG D:ASP220 2.8 38.6 1.0 OD1 D:ASP220 2.9 40.9 1.0 C1 D:HL6318 3.0 66.1 0.8 CD2 D:HIS123 3.0 36.8 1.0 CG D:ASP122 3.1 42.0 1.0 CE1 D:HIS266 3.2 36.4 1.0 CD2 D:HIS266 3.3 34.1 1.0 CE1 D:HIS123 3.3 39.1 1.0 OD1 D:ASP122 3.5 38.7 1.0 O1 D:HL6318 3.6 51.4 0.8 CO D:CO301 3.7 43.4 1.0 C3 D:HL6318 3.8 49.0 0.8 C4 D:HL6318 3.8 57.2 0.8 CG D:HIS123 4.2 36.2 1.0 CB D:ASP220 4.3 34.9 1.0 ND1 D:HIS266 4.4 32.8 1.0 ND1 D:HIS123 4.4 35.9 1.0 NE2 D:HIS118 4.4 32.6 1.0 CG D:HIS266 4.4 34.8 1.0 CE1 D:TYR223 4.4 38.9 1.0 CB D:ASP122 4.5 39.5 1.0 CE1 D:HIS118 4.5 36.4 1.0

M.Corbella, J.Bravo, A.O.Demkiv, A.R.Calixto, K.Sompiyachoke, C.Bergonzi, A.R.Brownless, M.H.Elias, S.C.L.Kamerlin. Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. Jacs Au V. 4 3519 2024.
ISSN: ESSN 2691-3704
PubMed: 39328773
DOI: 10.1021/JACSAU.4C00404