Iron 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:

Cobalt

(Co)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Center, PDB code: 9b2l:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe306 b:51.6 occ:1.00 NE2 A:HIS123 2.0 44.9 1.0 NE2 A:HIS266 2.1 45.7 1.0 O A:HOH449 2.2 46.5 1.0 OD2 A:ASP220 2.3 55.2 1.0 O A:HOH411 2.4 55.3 1.0 OD1 A:ASN122 2.5 68.2 1.0 CD2 A:HIS123 2.9 47.2 1.0 OD1 A:ASP220 2.9 46.5 1.0 CG A:ASP220 2.9 51.2 1.0 CE1 A:HIS266 3.0 47.7 1.0 CE1 A:HIS123 3.1 45.8 1.0 CD2 A:HIS266 3.2 50.3 1.0 CG A:ASN122 3.2 51.0 1.0 ND2 A:ASN122 3.3 59.0 1.0 O A:HOH430 3.4 49.6 1.0 CO A:CO307 3.4 48.4 1.0 CG A:HIS123 4.1 42.4 1.0 ND1 A:HIS266 4.1 47.3 1.0 ND1 A:HIS123 4.1 36.7 1.0 CG A:HIS266 4.2 52.5 1.0 CE1 A:HIS118 4.3 47.6 1.0 NE2 A:HIS118 4.3 48.2 1.0 CB A:ASP220 4.4 55.4 1.0 CE1 A:TYR223 4.5 51.9 1.0 CB A:ASN122 4.7 52.6 1.0 NE2 A:HIS198 5.0 45.6 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe405 b:49.9 occ:1.00 NE2 B:HIS123 2.0 46.6 1.0 NE2 B:HIS266 2.1 42.7 1.0 OD2 B:ASP220 2.2 60.1 1.0 O B:HOH551 2.3 45.9 1.0 O B:HOH507 2.3 56.5 1.0 OD1 B:ASN122 2.4 62.0 1.0 OD1 B:ASP220 2.9 49.5 1.0 CG B:ASP220 2.9 51.6 1.0 CD2 B:HIS123 2.9 48.5 1.0 CE1 B:HIS123 3.0 46.2 1.0 CE1 B:HIS266 3.0 44.8 1.0 CD2 B:HIS266 3.1 48.4 1.0 CG B:ASN122 3.2 51.2 1.0 ND2 B:ASN122 3.4 59.1 1.0 O B:HOH531 3.4 49.4 1.0 CO B:CO406 3.4 47.4 1.0 CG B:HIS123 4.1 43.4 1.0 ND1 B:HIS123 4.1 36.4 1.0 ND1 B:HIS266 4.2 46.2 1.0 CG B:HIS266 4.3 49.1 1.0 CE1 B:HIS118 4.3 47.9 1.0 CB B:ASP220 4.4 52.1 1.0 NE2 B:HIS118 4.4 48.1 1.0 CE1 B:TYR223 4.4 52.7 1.0 CB B:ASN122 4.6 53.3 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