Cobalt 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:

Iron

(Fe)

2 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase Gcl Bound to N-Hexanoyl-L- Homoserine Lactone, PDB code: 9ayt:
Jump to Cobalt binding site number: 1; 2;

Cobalt 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 Cobalt with other atoms in the Co 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:Co301 b:43.9 occ:1.00 O P:HOH410 2.1 41.8 1.0 NE2 P:HIS118 2.2 33.2 1.0 ND1 P:HIS120 2.2 34.4 1.0 NE2 P:HIS198 2.3 34.1 1.0 OD2 P:ASP220 2.4 40.3 1.0 O1 P:HL6315 2.6 49.9 0.8 CD2 P:HIS118 3.0 32.0 1.0 CD2 P:HIS198 3.1 37.8 1.0 CE1 P:HIS120 3.1 37.2 1.0 CG P:HIS120 3.2 33.9 1.0 CE1 P:HIS118 3.2 35.5 1.0 CE1 P:HIS198 3.3 37.2 1.0 C1 P:HL6315 3.4 64.9 0.8 CG P:ASP220 3.5 40.3 1.0 CB P:HIS120 3.5 31.9 1.0 FE P:FE302 3.6 39.6 1.0 CB P:ASP220 3.8 34.6 1.0 O2 P:HL6315 3.8 39.6 0.8 O3 P:HL6315 4.2 71.6 0.8 CG P:HIS118 4.2 33.3 1.0 CD2 P:HIS123 4.3 36.9 1.0 NE2 P:HIS120 4.3 34.0 1.0 ND1 P:HIS118 4.3 33.2 1.0 C4 P:HL6315 4.3 65.0 0.8 NE2 P:HIS123 4.3 33.9 1.0 CG P:HIS198 4.3 34.2 1.0 CD2 P:HIS120 4.3 36.8 1.0 ND1 P:HIS198 4.4 38.4 1.0 OD1 P:ASP122 4.5 40.5 1.0 OD1 P:ASP220 4.6 41.8 1.0 C5 P:HL6315 4.7 80.3 0.8 OH P:TYR223 4.8 38.5 1.0 C9 P:HL6315 4.8 72.5 0.8 N P:HL6315 4.9 81.3 0.8 OD2 P:ASP122 4.9 38.5 1.0 CA P:HIS120 5.0 32.3 1.0

Cobalt 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 Cobalt with other atoms in the Co 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:Co301 b:43.4 occ:1.00 O D:HOH401 2.1 42.6 1.0 NE2 D:HIS118 2.2 32.6 1.0 ND1 D:HIS120 2.2 34.1 1.0 NE2 D:HIS198 2.3 32.8 1.0 OD2 D:ASP220 2.4 41.2 1.0 O1 D:HL6318 2.6 51.4 0.8 CD2 D:HIS118 3.0 29.6 1.0 CD2 D:HIS198 3.1 36.9 1.0 CE1 D:HIS120 3.1 35.5 1.0 CG D:HIS120 3.2 30.5 1.0 CE1 D:HIS118 3.3 36.4 1.0 CE1 D:HIS198 3.3 34.7 1.0 C1 D:HL6318 3.4 66.1 0.8 CG D:ASP220 3.4 38.6 1.0 CB D:HIS120 3.5 33.7 1.0 O2 D:HL6318 3.7 42.1 0.8 FE D:FE302 3.7 39.8 1.0 CB D:ASP220 3.8 34.9 1.0 CG D:HIS118 4.2 32.9 1.0 NE2 D:HIS120 4.3 33.1 1.0 CD2 D:HIS123 4.3 36.8 1.0 ND1 D:HIS118 4.3 33.9 1.0 CG D:HIS198 4.3 35.2 1.0 CD2 D:HIS120 4.3 35.7 1.0 NE2 D:HIS123 4.3 34.7 1.0 ND1 D:HIS198 4.4 35.0 1.0 OD1 D:ASP122 4.4 38.7 1.0 O3 D:HL6318 4.5 68.0 0.8 OD1 D:ASP220 4.6 40.9 1.0 C4 D:HL6318 4.6 57.2 0.8 OH D:TYR223 4.7 37.3 1.0 OD2 D:ASP122 5.0 37.3 1.0 C10 D:HL6318 5.0 66.7 0.8

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