Chlorine in PDB 7mdf: Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog

All present enzymatic activity of Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog:
3.5.2.6;

The structure of Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog, PDB code: 7mdf was solved by J.A.Velilla, M.R.Volpe, R.Gaudet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.74 / 2.30
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.686, 96.686, 182.736, 90, 90, 90
R / Rfree (%)	19.1 / 21.9

The structure of Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Chlorine atom in the Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog (pdb code 7mdf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog, PDB code: 7mdf:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl715 b:76.2 occ:1.00 NH2 A:ARG255 3.3 50.1 1.0 CD A:LYS227 3.6 64.7 1.0 CE A:LYS227 3.9 79.6 1.0 O A:HOH1051 4.1 71.0 1.0 O A:HOH940 4.4 45.5 1.0 CZ A:ARG255 4.6 70.6 1.0 CG2 A:THR205 4.8 37.9 1.0

Chlorine binding site 2 out of 3 in the Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl716 b:115.7 occ:1.00 O A:HOH992 3.2 53.1 1.0 CD2 A:HIS279 3.9 57.7 1.0 CA A:HIS279 4.0 54.7 1.0 CB A:HIS279 4.2 43.7 1.0 CB A:LYS281 4.3 70.5 1.0 N A:ARG280 4.3 53.0 1.0 N A:LYS281 4.4 61.1 1.0 CG A:HIS279 4.5 53.5 1.0 C A:HIS279 4.5 45.8 1.0 O A:LEU278 4.5 41.2 1.0 CA A:LYS281 5.0 64.0 1.0

Chlorine binding site 3 out of 3 in the Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl717 b:71.6 occ:1.00 O A:HOH810 3.1 58.6 1.0 NH1 A:ARG113 3.2 68.7 1.0 NH1 A:ARG213 3.3 66.0 1.0 NZ A:LYS204 3.8 67.1 1.0 NH2 A:ARG213 3.9 76.8 1.0 CE A:LYS204 4.0 56.3 1.0 CZ A:ARG213 4.0 61.2 1.0 CD A:LYS204 4.1 58.7 1.0 CZ A:ARG113 4.3 75.3 1.0 CB A:THR202 4.5 43.3 1.0 CG2 A:THR202 4.5 34.9 1.0 NH2 A:ARG113 4.5 70.9 1.0 O A:THR202 4.9 54.3 1.0 CA A:THR202 4.9 47.3 1.0

J.A.Velilla, M.R.Volpe, G.E.Kenney, R.M.Walsh Jr., E.P.Balskus, R.Gaudet. Structural Basis of Colibactin Activation By the Clbp Peptidase. Nat.Chem.Biol. 2022.
ISSN: ESSN 1552-4469
PubMed: 36253550
DOI: 10.1038/S41589-022-01142-Z