Zinc 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:

Fluorine	(F)	4 atoms
Calcium	(Ca)	5 atoms

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

Zinc binding site 1 out of 2 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ulilysin - C269A with Aebsf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:20.2 occ:1.00 OXT B:SER403 1.8 46.7 1.0 NE2 A:HIS228 2.2 21.4 1.0 NE2 A:HIS238 2.2 24.3 1.0 NE2 A:HIS232 2.2 23.9 1.0 C B:SER403 2.5 46.7 1.0 O B:SER403 2.5 46.6 1.0 CD2 A:HIS238 3.0 24.4 1.0 CD2 A:HIS228 3.0 22.3 1.0 CD2 A:HIS232 3.0 22.2 1.0 CE1 A:HIS228 3.2 21.7 1.0 CE1 A:HIS238 3.3 26.6 1.0 CE1 A:HIS232 3.3 23.2 1.0 CE1 A:TYR292 3.8 27.9 1.0 CA B:SER403 3.9 46.8 1.0 OH A:TYR292 4.0 29.7 1.0 CG A:HIS238 4.2 24.4 1.0 N B:SER403 4.2 46.8 1.0 CG A:HIS228 4.2 21.1 1.0 CG A:HIS232 4.2 20.6 1.0 ND1 A:HIS228 4.3 22.4 1.0 ND1 A:HIS238 4.3 23.4 1.0 ND1 A:HIS232 4.3 19.9 1.0 O B:GLY401 4.3 46.6 1.0 CZ A:TYR292 4.4 29.3 1.0 C B:SER402 4.5 46.7 1.0 OE1 A:GLU229 4.5 25.1 1.0 O B:SER402 4.5 46.6 1.0 OE2 A:GLU229 4.6 27.3 1.0 CD1 A:TYR292 4.8 26.6 1.0 CD A:GLU229 4.8 23.7 1.0 CB B:SER403 4.9 47.0 1.0 CE A:MET290 4.9 20.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ulilysin - C269A with Aebsf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:21.1 occ:1.00 OXT D:SER403 1.8 43.8 1.0 NE2 C:HIS228 2.1 22.2 1.0 NE2 C:HIS238 2.2 26.3 1.0 NE2 C:HIS232 2.2 23.7 1.0 C D:SER403 2.5 43.8 1.0 O D:SER403 2.5 43.7 1.0 CD2 C:HIS238 3.0 25.0 1.0 CD2 C:HIS228 3.0 22.6 1.0 CD2 C:HIS232 3.1 22.9 1.0 CE1 C:HIS228 3.2 24.8 1.0 CE1 C:HIS238 3.2 28.0 1.0 CE1 C:HIS232 3.3 23.4 1.0 CE1 C:TYR292 3.8 28.6 1.0 CA D:SER403 3.9 43.9 1.0 OH C:TYR292 4.0 32.7 1.0 N D:SER403 4.1 43.9 1.0 CG C:HIS238 4.2 23.3 1.0 CG C:HIS228 4.2 22.4 1.0 ND1 C:HIS238 4.2 24.3 1.0 ND1 C:HIS228 4.2 21.4 1.0 CG C:HIS232 4.3 21.2 1.0 O D:GLY401 4.3 43.7 1.0 ND1 C:HIS232 4.3 21.7 1.0 CZ C:TYR292 4.3 28.2 1.0 C D:SER402 4.4 43.8 1.0 OE1 C:GLU229 4.5 26.0 1.0 O D:SER402 4.5 43.7 1.0 OE2 C:GLU229 4.5 29.4 1.0 CD1 C:TYR292 4.8 27.3 1.0 CD C:GLU229 4.8 22.1 1.0 CB D:SER403 4.9 44.1 1.0 CE C:MET290 4.9 21.8 1.0 C2 C:AES404 5.0 28.4 0.5 C D:GLY401 5.0 43.8 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