Fluorine in PDB 8cd8: Ulilysin - C269A with Aebsf Complex

The structure of Ulilysin - C269A with Aebsf Complex, PDB code: 8cd8 was solved by A.Rodriguez-Banqueri, U.Eckhard, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.33 / 1.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.13, 124.66, 86.9, 90, 90, 90
R / Rfree (%)	20.7 / 24.3

The structure of Ulilysin - C269A with Aebsf Complex also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	5 atoms

The binding sites of Fluorine atom in the Ulilysin - C269A with Aebsf Complex (pdb code 8cd8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ulilysin - C269A with Aebsf Complex, PDB code: 8cd8:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ulilysin - C269A with Aebsf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:30.4 occ:0.49 F A:AES404 0.0 30.4 0.5 S A:AES404 1.5 29.7 0.5 O1S A:AES404 2.4 29.5 0.5 O2S A:AES404 2.4 34.1 0.5 O1S A:AES404 2.5 34.1 0.5 O A:GLY189 2.8 21.6 1.0 C1 A:AES404 2.8 28.3 0.5 O2S A:AES404 2.9 29.7 0.5 C2 A:AES404 3.0 27.8 0.5 S A:AES404 3.0 31.0 0.5 C2 A:AES404 3.1 27.7 0.5 O B:SER403 3.3 46.6 1.0 N A:GLY189 3.4 21.8 1.0 CB B:SER403 3.4 47.0 1.0 C1 A:AES404 3.4 28.6 0.5 OE2 A:GLU229 3.6 27.3 1.0 C B:SER403 3.7 46.7 1.0 C A:GLY189 3.7 23.9 1.0 N A:LEU188 3.7 23.5 1.0 CA B:SER403 3.8 46.8 1.0 C6 A:AES404 4.0 28.7 0.5 CB A:ILE187 4.0 26.7 1.0 CA A:GLY189 4.1 21.9 1.0 OG B:SER403 4.1 47.2 1.0 C3 A:AES404 4.2 27.9 0.5 C A:LEU188 4.3 23.4 1.0 CA A:LEU188 4.3 23.4 1.0 CB A:LEU188 4.4 24.0 1.0 F A:AES404 4.5 33.8 0.5 C3 A:AES404 4.5 27.4 0.5 OXT B:SER403 4.5 46.7 1.0 C A:ILE187 4.6 24.8 1.0 CA A:ILE187 4.7 24.1 1.0 OH A:TYR292 4.7 29.7 1.0 CG2 A:ILE187 4.8 26.5 1.0 CD A:GLU229 4.8 23.7 1.0 CD1 A:ILE187 4.8 28.2 1.0 CG1 A:ILE187 4.8 27.3 1.0 C6 A:AES404 4.8 29.7 0.5 N A:TYR190 4.9 21.0 1.0 CE1 A:TYR292 5.0 27.9 1.0

Fluorine binding site 2 out of 4 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ulilysin - C269A with Aebsf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:33.8 occ:0.51 F A:AES404 0.0 33.8 0.5 S A:AES404 1.5 31.0 0.5 O1S A:AES404 2.4 34.1 0.5 O2S A:AES404 2.4 29.7 0.5 O2S A:AES404 2.7 34.1 0.5 O1S A:AES404 2.7 29.5 0.5 C1 A:AES404 2.8 28.6 0.5 O A:HOH749 2.9 38.6 1.0 S A:AES404 3.0 29.7 0.5 O A:HOH822 3.1 42.3 1.0 C6 A:AES404 3.1 28.7 0.5 C6 A:AES404 3.1 29.7 0.5 C1 A:AES404 3.5 28.3 0.5 C2 A:AES404 4.1 27.8 0.5 O A:HOH821 4.2 42.4 1.0 C5 A:AES404 4.3 28.3 0.5 F A:AES404 4.5 30.4 0.5 CE2 A:TYR292 4.5 27.0 1.0 C5 A:AES404 4.5 28.1 0.5 CZ A:TYR292 4.6 29.3 1.0 CD2 A:TYR292 4.7 27.2 1.0 CE2 A:PHE267 4.8 30.7 1.0 C2 A:AES404 4.9 27.7 0.5 CA A:ILE187 5.0 24.1 1.0 CG2 A:ILE187 5.0 26.5 1.0

Fluorine binding site 3 out of 4 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ulilysin - C269A with Aebsf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F404 b:30.5 occ:0.50 F C:AES404 0.0 30.5 0.5 S C:AES404 1.5 31.9 0.5 O2S C:AES404 1.9 31.2 0.5 O2S C:AES404 2.4 33.3 0.5 O1S C:AES404 2.4 30.7 0.5 C1 C:AES404 2.8 29.1 0.5 C2 C:AES404 2.8 28.6 0.5 O C:GLY189 2.8 22.5 1.0 S C:AES404 2.9 32.9 0.5 C2 C:AES404 3.1 28.4 0.5 N C:GLY189 3.2 23.5 1.0 C1 C:AES404 3.3 29.5 0.5 O1S C:AES404 3.4 33.4 0.5 N C:LEU188 3.4 23.7 1.0 O D:SER403 3.6 43.7 1.0 OE2 C:GLU229 3.7 29.4 1.0 CB D:SER403 3.7 44.1 1.0 C C:GLY189 3.7 23.5 1.0 CB C:ILE187 3.9 26.6 1.0 C D:SER403 4.0 43.8 1.0 C6 C:AES404 4.0 29.8 0.5 C C:LEU188 4.0 22.2 1.0 CA C:LEU188 4.0 24.2 1.0 CA C:GLY189 4.0 21.7 1.0 C3 C:AES404 4.0 28.1 0.5 CB C:LEU188 4.1 23.8 1.0 CA D:SER403 4.1 43.9 1.0 F C:AES404 4.2 33.6 0.5 C C:ILE187 4.3 25.1 1.0 OG D:SER403 4.3 46.1 1.0 CA C:ILE187 4.5 26.0 1.0 C3 C:AES404 4.5 27.2 0.5 C6 C:AES404 4.7 30.2 0.5 CG2 C:ILE187 4.7 29.7 1.0 CG1 C:ILE187 4.7 28.6 1.0 OXT D:SER403 4.8 43.8 1.0 CD1 C:ILE187 4.9 28.9 1.0 CG C:LEU188 4.9 28.4 1.0 CD C:GLU229 4.9 22.1 1.0 N C:TYR190 4.9 19.9 1.0 OH C:TYR292 5.0 32.7 1.0

Fluorine binding site 4 out of 4 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ulilysin - C269A with Aebsf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F404 b:33.6 occ:0.50 F C:AES404 0.0 33.6 0.5 S C:AES404 1.6 32.9 0.5 O1S C:AES404 2.0 30.7 0.5 O2S C:AES404 2.4 31.2 0.5 O1S C:AES404 2.4 33.4 0.5 O C:HOH820 2.8 41.5 1.0 C1 C:AES404 2.8 29.5 0.5 S C:AES404 2.9 31.9 0.5 O2S C:AES404 3.2 33.3 0.5 C6 C:AES404 3.2 29.8 0.5 C6 C:AES404 3.2 30.2 0.5 O C:HOH518 3.2 40.1 1.0 O C:HOH815 3.4 44.9 1.0 C1 C:AES404 3.5 29.1 0.5 C2 C:AES404 4.0 28.6 0.5 F C:AES404 4.2 30.5 0.5 CA C:ILE187 4.4 26.0 1.0 N C:LEU188 4.4 23.7 1.0 C5 C:AES404 4.4 29.3 0.5 O C:ASP186 4.5 32.0 1.0 CG C:LEU188 4.6 28.4 1.0 C5 C:AES404 4.6 28.9 0.5 CB C:ILE187 4.7 26.6 1.0 CG2 C:ILE187 4.8 29.7 1.0 CD1 C:LEU188 4.9 28.4 1.0 C2 C:AES404 4.9 28.4 0.5 C C:ILE187 4.9 25.1 1.0

A.Rodriguez-Banqueri, M.Moliner-Culubret, S.R.Mendes, T.Guevara, U.Eckhard, F.X.Gomis-Ruth. Structural Insights Into Latency of the Metallopeptidase Ulilysin (Lysarginase) and Its Unexpected Inhibition By A Sulfonyl-Fluoride Inhibitor of Serine Peptidases. Dalton Trans V. 52 3610 2023.
ISSN: ESSN 1477-9234
PubMed: 36857690
DOI: 10.1039/D3DT00458A