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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

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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

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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: Fri Jul 19 07:35:39 2024

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