Chlorine in PDB 9dfg: Crystal Structure of Prnb in Complex with 7-Cl-Trp

The structure of Crystal Structure of Prnb in Complex with 7-Cl-Trp, PDB code: 9dfg was solved by B.Li, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.63 / 2.42
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.011, 122.52, 66.739, 90, 94.64, 90
R / Rfree (%)	18.1 / 23.4

The structure of Crystal Structure of Prnb in Complex with 7-Cl-Trp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Prnb in Complex with 7-Cl-Trp (pdb code 9dfg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Prnb in Complex with 7-Cl-Trp, PDB code: 9dfg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Prnb in Complex with 7-Cl-Trp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Prnb in Complex with 7-Cl-Trp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:53.1 occ:1.00 CL A:CTE605 0.0 53.1 1.0 CZ2 A:CTE605 1.7 43.2 1.0 CE2 A:CTE605 2.7 35.8 1.0 CH2 A:CTE605 2.7 36.0 1.0 CD2 A:TYR104 3.1 32.8 1.0 NE1 A:CTE605 3.2 37.3 1.0 CE2 A:TYR104 3.4 33.0 1.0 CE1 A:PHE195 3.5 30.8 1.0 CZ A:PHE195 3.8 37.7 1.0 O A:ALA208 3.9 32.4 1.0 CB A:ALA208 4.0 27.4 1.0 C A:ALA208 4.0 34.7 1.0 CZ3 A:CTE605 4.0 34.8 1.0 CD2 A:CTE605 4.1 34.0 1.0 CG A:TYR104 4.1 38.2 1.0 CD1 A:PHE195 4.2 31.3 1.0 N A:GLY209 4.2 32.3 1.0 OG A:SER101 4.2 46.9 1.0 CA A:GLY209 4.4 31.0 1.0 CD1 A:CTE605 4.5 36.9 1.0 CB A:TYR104 4.6 30.3 1.0 CE3 A:CTE605 4.6 33.4 1.0 CZ A:TYR104 4.6 35.4 1.0 CA A:ALA208 4.7 28.7 1.0 CE2 A:PHE195 4.7 32.1 1.0 C A:GLY209 4.7 36.1 1.0 N A:GLY210 4.8 34.9 1.0 CB A:LEU126 5.0 34.0 1.0 CG A:PHE195 5.0 30.8 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Prnb in Complex with 7-Cl-Trp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Prnb in Complex with 7-Cl-Trp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl704 b:47.9 occ:1.00 CL B:CTE704 0.0 47.9 1.0 CZ2 B:CTE704 1.7 40.5 1.0 CH2 B:CTE704 2.7 31.4 1.0 CE2 B:CTE704 2.7 32.4 1.0 CD2 B:TYR104 3.2 29.4 1.0 NE1 B:CTE704 3.3 32.8 1.0 CE2 B:TYR104 3.6 33.7 1.0 CE1 B:PHE195 3.7 33.2 1.0 O B:ALA208 3.8 34.5 1.0 CB B:ALA208 3.8 28.0 1.0 C B:ALA208 3.9 38.0 1.0 N B:GLY209 4.0 30.8 1.0 CZ3 B:CTE704 4.0 33.6 1.0 CD2 B:CTE704 4.1 30.2 1.0 CZ B:PHE195 4.1 31.5 1.0 CG B:TYR104 4.2 30.4 1.0 CD1 B:PHE195 4.2 30.4 1.0 CA B:GLY209 4.3 36.2 1.0 C B:GLY209 4.5 38.4 1.0 CA B:ALA208 4.5 31.7 1.0 CB B:SER101 4.5 32.3 1.0 CB B:TYR104 4.6 30.7 1.0 CE3 B:CTE704 4.6 34.4 1.0 CD1 B:CTE704 4.6 33.9 1.0 N B:GLY210 4.7 33.1 1.0 CA B:SER101 4.8 31.9 1.0 CZ B:TYR104 4.8 34.3 1.0 CE2 B:PHE195 4.9 27.6 1.0 O B:GLY209 4.9 36.0 1.0

B.Li, R.Usai, J.Campbell, Y.Wang. Elucidating Ligand Interactions and Small-Molecule Activation in the Pyrrolnitrin Biosynthetic Enzyme Prnb. J.Biol.Chem. V. 301 08123 2025.
ISSN: ESSN 1083-351X
PubMed: 39725034
DOI: 10.1016/J.JBC.2024.108123