Cobalt in PDB 9b2j: Structure of the Quorum Quenching Lactonase Gcl I237M Mutant

All present enzymatic activity of Structure of the Quorum Quenching Lactonase Gcl I237M Mutant:
3.1.1.81;

The structure of Structure of the Quorum Quenching Lactonase Gcl I237M Mutant, PDB code: 9b2j 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)	64.17 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.4, 110.3, 79.4, 90, 115.9, 90
R / Rfree (%)	18.4 / 19.9

The structure of Structure of the Quorum Quenching Lactonase Gcl I237M Mutant also contains other interesting chemical elements:

Iron

(Fe)

3 atoms

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase Gcl I237M Mutant (pdb code 9b2j). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase Gcl I237M Mutant, PDB code: 9b2j:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl I237M Mutant


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 I237M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:25.4 occ:0.90 ND1 A:HIS120 2.1 25.9 1.0 OD2 A:ASP220 2.2 36.6 1.0 NE2 A:HIS118 2.2 24.4 1.0 NE2 A:HIS198 2.2 24.5 1.0 O A:HOH478 2.3 42.0 1.0 O A:HOH407 2.4 38.5 1.0 CE1 A:HIS120 3.0 25.6 1.0 CD2 A:HIS118 3.1 22.7 1.0 CG A:HIS120 3.2 26.6 1.0 CE1 A:HIS198 3.2 26.6 1.0 CD2 A:HIS198 3.2 24.9 1.0 CG A:ASP220 3.2 35.6 1.0 CE1 A:HIS118 3.2 24.0 1.0 FE A:FE309 3.4 40.3 1.0 CB A:HIS120 3.6 26.5 1.0 CB A:ASP220 3.6 31.2 1.0 O A:HOH544 3.9 36.7 1.0 NE2 A:HIS123 4.1 25.6 1.0 NE2 A:HIS120 4.1 24.0 1.0 CD2 A:HIS123 4.2 23.9 1.0 CD2 A:HIS120 4.2 22.8 1.0 CG A:HIS118 4.3 23.5 1.0 ND1 A:HIS198 4.3 27.7 1.0 ND1 A:HIS118 4.3 23.8 1.0 OD1 A:ASP220 4.3 37.9 1.0 CG A:HIS198 4.4 24.5 1.0 OD1 A:ASP122 4.4 35.9 1.0 OH A:TYR223 4.5 30.4 1.0 SD A:MET237 4.8 65.3 0.5 CE1 A:TYR223 4.9 25.3 1.0

Cobalt binding site 2 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl I237M Mutant


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 I237M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:22.5 occ:0.90 ND1 B:HIS120 2.0 23.8 1.0 OD2 B:ASP220 2.1 23.9 1.0 NE2 B:HIS118 2.1 24.2 1.0 O B:HOH415 2.2 31.0 1.0 NE2 B:HIS198 2.3 24.9 1.0 O B:HOH497 2.3 29.8 1.0 CE1 B:HIS120 2.9 26.8 1.0 CD2 B:HIS118 3.0 22.5 1.0 CG B:HIS120 3.1 25.1 1.0 CD2 B:HIS198 3.2 24.9 1.0 CE1 B:HIS118 3.2 25.7 1.0 CG B:ASP220 3.2 27.2 1.0 CE1 B:HIS198 3.3 26.1 1.0 CB B:HIS120 3.5 25.2 1.0 FE B:FE311 3.6 35.9 1.0 CB B:ASP220 3.7 25.5 1.0 O B:HOH588 3.9 35.6 1.0 NE2 B:HIS120 4.1 27.7 1.0 NE2 B:HIS123 4.2 30.1 1.0 CD2 B:HIS120 4.2 25.3 1.0 CG B:HIS118 4.2 23.4 1.0 CD2 B:HIS123 4.2 26.7 1.0 ND1 B:HIS118 4.3 22.6 1.0 OD1 B:ASP220 4.3 20.4 1.0 CG B:HIS198 4.3 23.7 1.0 ND1 B:HIS198 4.3 25.1 1.0 OD1 B:ASP122 4.6 27.7 1.0 OH B:TYR223 4.7 27.3 1.0 O B:HOH626 4.9 46.3 1.0

Cobalt binding site 3 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl I237M Mutant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Quorum Quenching Lactonase Gcl I237M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Co304 b:21.4 occ:0.90 O C:HOH458 2.0 27.9 1.0 ND1 C:HIS120 2.1 25.3 1.0 NE2 C:HIS118 2.2 24.6 1.0 OD2 C:ASP220 2.2 27.9 1.0 O C:HOH409 2.3 27.6 1.0 NE2 C:HIS198 2.3 21.2 1.0 CE1 C:HIS120 3.0 26.1 1.0 CD2 C:HIS118 3.0 21.2 1.0 CG C:HIS120 3.2 25.3 1.0 CE1 C:HIS118 3.2 23.5 1.0 CD2 C:HIS198 3.2 21.8 1.0 CG C:ASP220 3.2 27.9 1.0 CE1 C:HIS198 3.3 26.1 1.0 FE C:FE310 3.5 35.3 1.0 CB C:HIS120 3.6 23.6 1.0 CB C:ASP220 3.7 24.9 1.0 O C:HOH572 3.8 28.6 1.0 NE2 C:HIS120 4.2 24.9 1.0 NE2 C:HIS123 4.2 25.6 1.0 CG C:HIS118 4.2 22.6 1.0 CD2 C:HIS123 4.2 25.6 1.0 ND1 C:HIS118 4.3 21.7 1.0 CD2 C:HIS120 4.3 23.1 1.0 OD1 C:ASP220 4.4 25.2 1.0 ND1 C:HIS198 4.4 25.9 1.0 CG C:HIS198 4.4 22.7 1.0 OD1 C:ASP122 4.6 28.9 1.0 OH C:TYR223 4.7 26.4 1.0 CE C:MET237 4.9 57.3 0.5 CE1 C:TYR223 5.0 26.5 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