Atomistry » Calcium » PDB 8bt4-8clf » 8cd8
Atomistry »
  Calcium »
    PDB 8bt4-8clf »
      8cd8 »

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

Protein crystallography data

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

Other elements in 8cd8:

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

Zinc (Zn) 2 atoms
Fluorine (F) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ulilysin - C269A with Aebsf Complex (pdb code 8cd8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Ulilysin - C269A with Aebsf Complex, PDB code: 8cd8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8cd8

Go back to Calcium Binding Sites List in 8cd8
Calcium binding site 1 out of 5 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ulilysin - C269A with Aebsf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:25.8
occ:1.00
 O A:TRP240 2.2 24.6 1.0
O A:HOH561 2.3 28.0 1.0
O A:PRO249 2.3 30.7 1.0
O A:GLN262 2.4 28.3 1.0
O A:ALA263 2.5 28.6 1.0
OE1 A:GLU243 2.5 29.7 1.0
OE2 A:GLU243 2.5 29.1 1.0
CD A:GLU243 2.8 30.9 1.0
C A:ALA263 3.3 30.6 1.0
C A:TRP240 3.4 26.8 1.0
C A:PRO249 3.5 33.9 1.0
C A:GLN262 3.5 29.0 1.0
CA A:ALA263 3.5 27.3 1.0
N A:ALA263 4.0 30.1 1.0
CA A:TRP240 4.1 22.9 1.0
CB A:TRP240 4.2 25.5 1.0
CG A:GLU243 4.2 30.9 1.0
O A:HOH514 4.3 29.9 1.0
CA A:CYS250 4.3 35.0 1.0
N A:CYS250 4.3 33.5 1.0
O A:HOH613 4.3 25.0 1.0
CA A:PRO249 4.3 35.8 1.0
O A:ARG252 4.4 33.4 1.0
N A:GLY241 4.5 26.1 1.0
N A:ASP264 4.5 28.5 1.0
CA A:GLY241 4.6 27.9 1.0
C A:CYS250 4.7 34.6 1.0
CA A:GLN262 4.7 28.9 1.0
CD1 A:TRP240 4.8 25.1 1.0
N A:SER251 4.8 32.2 1.0
OD1 A:ASN261 4.8 33.3 1.0
N A:GLN262 4.9 29.8 1.0
N A:ARG252 4.9 31.2 1.0
CB A:ALA263 4.9 30.0 1.0
CG A:TRP240 4.9 24.9 1.0
CB A:PRO249 5.0 36.4 1.0

Calcium binding site 2 out of 5 in 8cd8

Go back to Calcium Binding Sites List in 8cd8
Calcium binding site 2 out of 5 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ulilysin - C269A with Aebsf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:26.6
occ:1.00
 OD2 A:ASP254 2.4 25.4 1.0
O A:THR259 2.4 27.3 1.0
O A:HOH709 2.4 33.3 1.0
O A:HOH601 2.4 27.9 0.4
O A:VAL256 2.4 31.5 1.0
O A:HOH588 2.5 27.0 1.0
OG1 A:THR259 2.5 28.3 1.0
O A:HOH601 2.5 27.0 0.6
O A:HOH540 2.6 27.2 1.0
CG A:ASP254 3.4 28.2 1.0
C A:THR259 3.4 26.6 1.0
CB A:THR259 3.6 26.2 1.0
C A:VAL256 3.6 28.9 1.0
OD1 A:ASP254 3.8 26.7 1.0
CA A:THR259 3.9 27.6 1.0
N A:THR259 4.1 27.6 1.0
N A:VAL256 4.2 27.8 1.0
CA A:VAL256 4.3 25.6 1.0
O A:PRO260 4.3 30.6 1.0
C A:PRO260 4.4 29.5 1.0
CB A:VAL256 4.5 26.4 1.0
N A:PRO260 4.5 29.3 1.0
N A:ASN261 4.6 29.2 1.0
N A:ASP254 4.6 29.1 1.0
O A:HOH503 4.6 37.4 1.0
O A:HOH744 4.6 34.1 1.0
CB A:ASP254 4.6 25.8 1.0
N A:ASP257 4.7 27.8 1.0
O A:ASP257 4.7 29.3 1.0
O A:HOH613 4.7 25.0 1.0
C A:ASP257 4.8 31.8 1.0
OG A:SER253 4.8 33.5 1.0
CA A:ASP257 4.8 29.4 1.0
CG2 A:THR259 4.8 25.3 1.0
CA A:PRO260 4.9 28.6 1.0
CA A:ASN261 4.9 30.2 1.0
O A:ILE239 5.0 23.1 1.0

Calcium binding site 3 out of 5 in 8cd8

Go back to Calcium Binding Sites List in 8cd8
Calcium binding site 3 out of 5 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ulilysin - C269A with Aebsf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:26.8
occ:1.00
 O C:HOH547 2.3 28.1 1.0
O C:TRP240 2.3 25.9 1.0
O C:PRO249 2.3 29.8 1.0
O C:GLN262 2.3 27.4 1.0
OE1 C:GLU243 2.5 30.7 1.0
O C:ALA263 2.5 27.1 1.0
OE2 C:GLU243 2.5 28.2 1.0
CD C:GLU243 2.8 30.4 1.0
C C:ALA263 3.3 30.2 1.0
C C:TRP240 3.5 25.8 1.0
C C:GLN262 3.5 28.8 1.0
C C:PRO249 3.5 33.7 1.0
CA C:ALA263 3.6 28.1 1.0
N C:ALA263 4.0 28.5 1.0
CA C:TRP240 4.1 25.3 1.0
O C:HOH534 4.2 30.7 1.0
CB C:TRP240 4.2 25.3 1.0
CG C:GLU243 4.3 31.9 1.0
CA C:CYS250 4.3 31.6 1.0
N C:CYS250 4.3 34.2 1.0
O C:ARG252 4.4 31.6 1.0
CA C:PRO249 4.4 35.3 1.0
O C:HOH587 4.4 26.7 1.0
N C:GLY241 4.5 27.1 1.0
N C:ASP264 4.6 27.0 1.0
CA C:GLY241 4.7 26.9 1.0
C C:CYS250 4.7 31.9 1.0
CD1 C:TRP240 4.7 27.3 1.0
CA C:GLN262 4.7 27.8 1.0
OD1 C:ASN261 4.8 30.8 1.0
N C:GLN262 4.8 27.6 1.0
N C:SER251 4.9 32.9 1.0
N C:ARG252 4.9 29.1 1.0
CG C:TRP240 4.9 25.8 1.0
SG C:CYS277 5.0 35.0 1.0
CB C:ALA263 5.0 30.0 1.0

Calcium binding site 4 out of 5 in 8cd8

Go back to Calcium Binding Sites List in 8cd8
Calcium binding site 4 out of 5 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ulilysin - C269A with Aebsf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:25.8
occ:1.00
 OD2 C:ASP254 2.3 25.6 1.0
O C:HOH616 2.3 26.4 1.0
O C:THR259 2.4 24.6 1.0
O C:HOH673 2.5 29.5 1.0
O C:VAL256 2.5 30.3 1.0
O C:HOH578 2.5 28.3 1.0
OG1 C:THR259 2.6 27.2 1.0
O C:HOH737 2.6 27.5 1.0
CG C:ASP254 3.4 24.6 1.0
C C:THR259 3.5 26.0 1.0
CB C:THR259 3.7 26.8 1.0
C C:VAL256 3.7 29.1 1.0
OD1 C:ASP254 3.8 24.7 1.0
CA C:THR259 4.0 25.3 1.0
N C:VAL256 4.2 28.4 1.0
N C:THR259 4.2 27.6 1.0
O C:PRO260 4.3 28.9 1.0
C C:PRO260 4.3 26.2 1.0
CA C:VAL256 4.4 24.3 1.0
O C:HOH755 4.4 33.3 1.0
O C:HOH681 4.5 37.1 1.0
N C:ASP254 4.5 26.3 1.0
N C:ASN261 4.5 27.2 1.0
O C:HOH591 4.5 38.3 1.0
O C:HOH587 4.5 26.7 1.0
N C:PRO260 4.5 27.3 1.0
CB C:ASP254 4.6 24.6 1.0
CB C:VAL256 4.6 26.4 1.0
N C:ASP257 4.7 28.3 1.0
OG C:SER253 4.7 29.7 1.0
O C:ASP257 4.8 28.8 1.0
O C:ILE239 4.8 23.2 1.0
CA C:ASN261 4.8 28.1 1.0
C C:ASP257 4.9 30.6 1.0
CA C:PRO260 4.9 27.6 1.0
CA C:ASP257 4.9 29.0 1.0
CA C:ASP254 4.9 26.2 1.0
CG2 C:THR259 4.9 25.7 1.0
N C:GLU255 5.0 26.7 1.0

Calcium binding site 5 out of 5 in 8cd8

Go back to Calcium Binding Sites List in 8cd8
Calcium binding site 5 out of 5 in the Ulilysin - C269A with Aebsf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ulilysin - C269A with Aebsf Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca405

b:20.6
occ:1.00
 O C:HOH701 2.3 28.0 1.0
O A:HOH685 2.3 26.9 1.0
OD2 C:ASP152 2.4 18.1 1.0
O A:HOH558 2.4 21.4 1.0
OD2 A:ASP152 2.4 19.8 1.0
O C:HOH537 2.4 21.9 1.0
CG C:ASP152 3.5 20.1 1.0
CG A:ASP152 3.5 20.5 1.0
CB C:ASP152 4.2 19.0 1.0
O C:SER151 4.2 19.6 1.0
O A:SER151 4.2 20.2 1.0
CB A:ASP152 4.2 20.9 1.0
O A:HOH633 4.2 20.5 1.0
O C:HOH647 4.2 21.2 1.0
OD1 C:ASP152 4.5 19.2 1.0
OD1 A:ASP152 4.5 19.2 1.0
C C:SER151 4.6 22.8 1.0
C A:SER151 4.6 23.4 1.0
OG1 A:THR200 4.7 20.7 1.0
OG1 C:THR200 4.7 17.6 1.0
O A:THR150 4.8 19.9 1.0
O C:THR150 4.8 21.9 1.0
CG2 A:THR200 4.8 18.2 1.0
O C:HOH792 4.9 34.5 1.0
CG2 C:THR200 4.9 18.9 1.0

Reference:

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
Page generated: Thu Jul 10 03:40:14 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy