Cobalt in PDB 9b2l: Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Center

All present enzymatic activity of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Center:
3.1.1.81;

The structure of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Center, PDB code: 9b2l 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)	73.89 / 2.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	109.22, 109.22, 221.66, 90, 90, 120
R / Rfree (%)	21.4 / 24.1

The structure of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Center 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 D122N Mutant - Bimetallic Center (pdb code 9b2l). 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 D122N Mutant - Bimetallic Center, PDB code: 9b2l:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Center


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 D122N Mutant - Bimetallic Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Co307 b:48.4 occ:1.00 O A:HOH411 2.0 55.3 1.0 NE2 A:HIS198 2.0 45.6 1.0 OD2 A:ASP220 2.0 55.2 1.0 NE2 A:HIS118 2.1 48.2 1.0 ND1 A:HIS120 2.1 46.0 1.0 O A:HOH430 2.4 49.6 1.0 CE1 A:HIS120 3.0 51.9 1.0 CD2 A:HIS198 3.0 39.6 1.0 CE1 A:HIS198 3.0 49.5 1.0 CD2 A:HIS118 3.1 44.2 1.0 CE1 A:HIS118 3.1 47.6 1.0 CG A:ASP220 3.1 51.2 1.0 CG A:HIS120 3.2 42.5 1.0 FE A:FE306 3.4 51.6 1.0 CB A:ASP220 3.6 55.4 1.0 CB A:HIS120 3.6 44.8 1.0 O A:HOH449 3.6 46.5 1.0 ND1 A:HIS198 4.1 46.3 1.0 NE2 A:HIS123 4.1 44.9 1.0 CG A:HIS198 4.1 42.2 1.0 NE2 A:HIS120 4.2 50.1 1.0 ND1 A:HIS118 4.2 44.3 1.0 CG A:HIS118 4.2 40.0 1.0 OD1 A:ASP220 4.2 46.5 1.0 CD2 A:HIS123 4.2 47.2 1.0 CD2 A:HIS120 4.3 50.3 1.0 ND2 A:ASN122 4.5 59.0 1.0 OH A:TYR223 4.5 54.0 1.0 CE1 A:TYR223 4.8 51.9 1.0

Cobalt binding site 2 out of 2 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Center


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 D122N Mutant - Bimetallic Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Co406 b:47.4 occ:1.00 OD2 B:ASP220 2.1 60.1 1.0 NE2 B:HIS198 2.1 42.7 1.0 ND1 B:HIS120 2.1 41.1 1.0 O B:HOH507 2.1 56.5 1.0 NE2 B:HIS118 2.1 48.1 1.0 O B:HOH531 2.5 49.4 1.0 CE1 B:HIS120 3.0 47.0 1.0 CE1 B:HIS198 3.0 49.8 1.0 CD2 B:HIS198 3.1 42.7 1.0 CE1 B:HIS118 3.1 47.9 1.0 CD2 B:HIS118 3.1 42.8 1.0 CG B:ASP220 3.2 51.6 1.0 CG B:HIS120 3.2 39.1 1.0 FE B:FE405 3.4 49.9 1.0 CB B:HIS120 3.6 41.6 1.0 CB B:ASP220 3.6 52.1 1.0 O B:HOH551 3.6 45.9 1.0 NE2 B:HIS123 4.1 46.6 1.0 NE2 B:HIS120 4.1 47.0 1.0 ND1 B:HIS198 4.1 48.9 1.0 CG B:HIS198 4.2 43.2 1.0 ND1 B:HIS118 4.2 47.1 1.0 CG B:HIS118 4.2 42.4 1.0 CD2 B:HIS120 4.2 48.1 1.0 CD2 B:HIS123 4.2 48.5 1.0 OD1 B:ASP220 4.2 49.5 1.0 OH B:TYR223 4.5 53.6 1.0 ND2 B:ASN122 4.5 59.1 1.0 CE1 B:TYR223 4.8 52.7 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