Bromine 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:

Chlorine

(Cl)

3 atoms

The binding sites of Bromine 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 Bromine atom.
In total 2 binding sites of Bromine where determined in the Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog, PDB code: 7mdf:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Full-Length S95A Clbp Bound to N-Acyl-D-Asparagine Analog


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br703 b:71.9 occ:0.71 BR25 A:Z9A703 0.0 71.9 0.7 C24 A:Z9A703 1.9 61.7 1.0 C23 A:Z9A703 2.9 58.1 1.0 C26 A:Z9A703 2.9 61.5 1.0 CG1 A:VAL471 3.8 73.2 1.0 CG2 A:THR386 3.9 66.5 1.0 C9 A:97N709 4.2 87.5 1.0 C22 A:Z9A703 4.2 48.7 1.0 CE2 A:PHE390 4.2 58.6 1.0 C27 A:Z9A703 4.2 50.0 1.0 CG2 A:ILE463 4.2 60.8 1.0 CZ A:PHE390 4.3 63.4 1.0 CA A:GLY467 4.3 48.1 1.0 CD A:PRO468 4.4 47.5 1.0 C11 A:97N709 4.6 85.9 1.0 C21 A:Z9A703 4.7 67.7 1.0 CB A:VAL471 4.8 69.2 1.0

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


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br704 b:63.5 occ:0.61 BR19 A:Z9G704 0.0 63.5 0.6 C18 A:Z9G704 1.9 52.9 1.0 C20 A:Z9G704 2.9 49.8 1.0 C17 A:Z9G704 2.9 55.9 1.0 C22 A:Z9A703 3.8 48.7 1.0 C23 A:Z9A703 4.0 58.1 1.0 CE2 A:PHE462 4.0 44.5 1.0 C21 A:Z9G704 4.2 44.5 1.0 C16 A:Z9G704 4.2 52.2 1.0 O3 A:AV0708 4.2 99.6 1.0 C11 A:97N709 4.3 85.9 1.0 O2 A:AV0708 4.3 105.2 1.0 C3 A:AV0708 4.3 100.4 1.0 C15 A:Z9G704 4.7 57.0 1.0 CD2 A:PHE462 4.7 49.8 1.0 CD1 A:LEU458 4.8 67.0 1.0 CZ A:PHE462 4.8 37.2 1.0 C21 A:Z9A703 4.8 67.7 1.0 C2 A:AV0708 4.8 102.5 1.0 CE2 A:PHE152 4.9 52.3 1.0 C12 A:97N709 5.0 77.8 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