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Calcium in PDB 5onr: Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin

Enzymatic activity of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin

All present enzymatic activity of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin, PDB code: 5onr was solved by J.P.Leite, L.Gales, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.37 / 1.39
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.696, 92.696, 129.368, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 19.9

Other elements in 5onr:

The structure of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin (pdb code 5onr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin, PDB code: 5onr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5onr

Go back to Calcium Binding Sites List in 5onr
Calcium binding site 1 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.7
occ:1.00
 O A:GLN61 2.3 13.8 1.0
O A:HOH749 2.3 17.2 1.0
OD1 A:ASP59 2.4 13.1 1.0
OD2 A:ASP57 2.4 14.2 1.0
O A:HOH598 2.4 14.7 1.0
O A:HOH556 2.4 17.7 1.0
OD1 A:ASP57 2.6 13.9 1.0
CG A:ASP57 2.8 14.7 1.0
CG A:ASP59 3.4 16.2 1.0
C A:GLN61 3.4 12.8 1.0
OD2 A:ASP59 3.7 19.7 1.0
O A:HOH661 3.9 19.8 1.0
N A:GLN61 3.9 12.9 1.0
CA A:GLN61 4.1 13.2 1.0
CB A:GLN61 4.3 16.4 1.0
CB A:ASP57 4.3 14.0 1.0
N A:ASP59 4.3 12.9 1.0
O A:HOH700 4.5 17.0 1.0
O A:HOH830 4.5 20.9 1.0
N A:PHE62 4.5 12.7 1.0
CB A:ASP59 4.6 13.6 1.0
OD2 A:ASP67 4.6 13.3 1.0
O A:HOH543 4.6 14.7 1.0
O A:HOH845 4.7 33.5 1.0
N A:ASN60 4.7 13.4 1.0
N A:ALA58 4.7 12.3 1.0
CA A:PHE62 4.8 12.4 1.0
CA A:ASP59 4.8 13.3 1.0
C A:ASP59 4.9 13.2 1.0
O A:HOH832 4.9 35.2 1.0

Calcium binding site 2 out of 4 in 5onr

Go back to Calcium Binding Sites List in 5onr
Calcium binding site 2 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:22.5
occ:1.00
 O A:ASN183 2.3 20.7 1.0
OE2 A:GLU190 2.4 16.3 1.0
OD2 A:ASP185 2.4 18.5 1.0
O A:HOH553 2.4 17.9 1.0
O A:HOH597 2.4 22.6 1.0
OE1 A:GLU177 2.6 15.9 1.0
CG A:ASP185 3.2 19.9 1.0
CD A:GLU190 3.3 13.9 1.0
CD A:GLU177 3.3 14.3 1.0
C A:ASN183 3.5 18.6 1.0
OD1 A:ASP185 3.6 15.6 1.0
CA A:CA403 3.7 14.0 1.0
OE2 A:GLU177 3.8 15.0 1.0
CG A:GLU190 3.8 15.5 1.0
N A:ASP185 4.1 17.0 1.0
CA A:PRO184 4.1 18.7 1.0
C A:PRO184 4.2 17.5 1.0
O A:HOH702 4.2 20.2 1.0
OD1 A:ASP191 4.2 20.0 1.0
CB A:ASN183 4.3 21.2 1.0
OD2 A:ASP191 4.3 17.7 1.0
N A:PRO184 4.3 15.8 1.0
OE1 A:GLU190 4.3 15.3 1.0
CB A:ASP185 4.3 16.2 1.0
CG A:GLU177 4.4 13.7 1.0
CA A:ASN183 4.5 19.6 1.0
CG A:ASP191 4.6 17.6 1.0
O A:HOH634 4.8 19.1 1.0
CA A:ASP185 4.9 15.6 1.0
O A:PRO184 4.9 20.3 1.0

Calcium binding site 3 out of 4 in 5onr

Go back to Calcium Binding Sites List in 5onr
Calcium binding site 3 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:14.0
occ:1.00
 O A:GLU187 2.3 13.5 1.0
OD2 A:ASP138 2.4 14.1 1.0
OE2 A:GLU190 2.4 16.3 1.0
OD1 A:ASP185 2.4 15.6 1.0
O A:HOH591 2.5 15.1 1.0
OE2 A:GLU177 2.5 15.0 1.0
OE1 A:GLU190 2.6 15.3 1.0
OE1 A:GLU177 2.6 15.9 1.0
CD A:GLU190 2.8 13.9 1.0
CD A:GLU177 2.9 14.3 1.0
CG A:ASP138 3.4 13.4 1.0
C A:GLU187 3.4 14.2 1.0
CG A:ASP185 3.4 19.9 1.0
CA A:CA402 3.7 22.5 1.0
OD2 A:ASP185 3.8 18.5 1.0
CB A:ASP138 4.0 11.2 1.0
O A:ASP185 4.1 15.1 1.0
N A:GLU187 4.2 16.8 1.0
O A:HOH634 4.2 19.1 1.0
OD1 A:ASP138 4.2 13.4 1.0
N A:ILE188 4.2 14.5 1.0
CA A:GLU187 4.3 16.1 1.0
CG A:GLU190 4.3 15.5 1.0
CG A:GLU177 4.4 13.7 1.0
CA A:ILE188 4.4 12.7 1.0
N A:GLY189 4.4 14.3 1.0
O A:HOH553 4.5 17.9 1.0
C A:ASP185 4.5 15.5 1.0
CB A:GLU187 4.6 19.1 1.0
N A:ASP185 4.6 17.0 1.0
CB A:ASP185 4.7 16.2 1.0
C A:ILE188 4.8 14.6 1.0
CB A:GLU177 4.9 14.7 1.0
CA A:ASP185 4.9 15.6 1.0
N A:GLU190 5.0 13.4 1.0

Calcium binding site 4 out of 4 in 5onr

Go back to Calcium Binding Sites List in 5onr
Calcium binding site 4 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:18.0
occ:1.00
 O A:TYR193 2.3 18.6 1.0
O A:ILE197 2.3 21.6 1.0
OD1 A:ASP200 2.4 18.9 1.0
O A:THR194 2.4 20.9 1.0
O A:HOH582 2.4 19.5 1.0
O A:HOH745 2.5 26.8 1.0
OG1 A:THR194 2.5 18.6 1.0
C A:THR194 3.2 19.1 1.0
C A:TYR193 3.3 17.5 1.0
CG A:ASP200 3.4 21.9 1.0
CB A:THR194 3.5 18.9 1.0
C A:ILE197 3.5 22.6 1.0
CA A:THR194 3.7 17.2 1.0
OD2 A:ASP200 3.8 21.0 1.0
N A:THR194 3.9 15.7 1.0
CA A:ILE197 4.3 21.5 1.0
N A:PRO195 4.3 18.5 1.0
CB A:ILE197 4.3 26.5 1.0
N A:ILE197 4.3 26.0 1.0
O A:HOH754 4.5 34.2 1.0
CA A:TYR193 4.5 15.3 1.0
O A:ASP200 4.5 18.5 1.0
N A:SER198 4.6 26.1 1.0
O A:GLU190 4.6 17.1 1.0
CB A:TYR193 4.6 16.1 1.0
N A:ASP200 4.7 20.1 1.0
CD2 A:TYR193 4.7 18.5 1.0
CA A:SER198 4.7 25.0 1.0
CA A:PRO195 4.7 21.1 1.0
CB A:ASP200 4.8 20.7 1.0
CG2 A:THR194 4.8 20.5 1.0
C A:ASP200 4.8 19.0 1.0
CG2 A:ILE197 4.9 22.4 1.0
CA A:ASP200 5.0 18.5 1.0
CG A:TYR193 5.0 18.0 1.0
N A:TYR193 5.0 14.8 1.0
C A:SER198 5.0 25.1 1.0

Reference:

J.P.Leite, L.Gales. Alzheimer'S A BETA1-40PEPTIDE Degradation By Thermolysin: Evidence of Inhibition By A C-Terminal A Beta Product. Febs Lett. V. 593 128 2019.
ISSN: ISSN 1873-3468
PubMed: 30403288
DOI: 10.1002/1873-3468.13285
Page generated: Mon Jul 15 09:51:48 2024

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