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

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

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

Protein crystallography data

The structure of Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd- Substituted Thermolysin, PDB code: 5onp 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) 38.63 / 1.34
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.412, 93.412, 130.149, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 18

Other elements in 5onp:

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

Cadmium (Cd) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 5onp

Go back to Calcium Binding Sites List in 5onp
Calcium binding site 1 out of 3 in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd- Substituted 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 Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:11.1
occ:1.00
 OE2 A:GLU190 2.3 13.6 1.0
OD1 A:ASP185 2.3 17.1 1.0
O A:ASN183 2.4 22.1 1.0
O A:HOH569 2.4 18.3 1.0
O A:HOH592 2.4 18.5 1.0
OE2 A:GLU177 2.5 13.5 1.0
CG A:ASP185 3.1 15.6 1.0
CD A:GLU190 3.2 14.7 1.0
CD A:GLU177 3.2 11.7 1.0
OD2 A:ASP185 3.5 13.4 1.0
C A:ASN183 3.6 23.1 1.0
OE1 A:GLU177 3.6 13.4 1.0
CA A:CA402 3.7 10.5 1.0
CG A:GLU190 3.7 14.9 1.0
N A:ASP185 4.1 15.1 1.0
CA A:PRO184 4.1 16.1 1.0
OE1 A:GLU190 4.2 13.5 1.0
OD1 A:ASP191 4.2 18.3 1.0
C A:PRO184 4.2 16.4 1.0
CG A:GLU177 4.3 13.7 1.0
CB A:ASP185 4.3 16.9 1.0
CB A:ASN183 4.3 26.4 1.0
O A:HOH501 4.3 38.2 1.0
N A:PRO184 4.3 17.4 1.0
OD2 A:ASP191 4.3 18.2 1.0
O A:HOH842 4.4 34.8 1.0
O A:HOH515 4.5 46.0 1.0
CA A:ASN183 4.6 29.1 1.0
CG A:ASP191 4.6 16.8 1.0
O A:LYS182 4.7 40.0 1.0
CA A:ASP185 4.8 13.0 1.0
O A:PRO184 4.9 17.4 1.0
O A:HOH636 4.9 17.5 1.0

Calcium binding site 2 out of 3 in 5onp

Go back to Calcium Binding Sites List in 5onp
Calcium binding site 2 out of 3 in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd- Substituted 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 Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:10.5
occ:1.00
 O A:GLU187 2.3 12.8 1.0
OD2 A:ASP138 2.4 11.9 1.0
O A:HOH595 2.4 13.9 1.0
OD2 A:ASP185 2.5 13.4 1.0
OE2 A:GLU190 2.5 13.6 1.0
OE1 A:GLU177 2.5 13.4 1.0
OE1 A:GLU190 2.5 13.5 1.0
OE2 A:GLU177 2.7 13.5 1.0
CD A:GLU190 2.8 14.7 1.0
CD A:GLU177 2.9 11.7 1.0
CG A:ASP138 3.4 12.5 1.0
C A:GLU187 3.4 13.5 1.0
CG A:ASP185 3.5 15.6 1.0
CA A:CA401 3.7 11.1 1.0
OD1 A:ASP185 3.9 17.1 1.0
CB A:ASP138 4.0 11.7 1.0
O A:ASP185 4.1 14.3 1.0
O A:HOH515 4.2 46.0 1.0
N A:ILE188 4.2 13.5 1.0
N A:GLU187 4.2 14.5 1.0
OD1 A:ASP138 4.3 14.5 1.0
CA A:GLU187 4.3 15.1 1.0
CA A:ILE188 4.3 12.8 1.0
CG A:GLU190 4.4 14.9 1.0
O A:HOH636 4.4 17.5 1.0
CG A:GLU177 4.4 13.7 1.0
N A:GLY189 4.4 11.6 1.0
CB A:GLU187 4.6 15.4 1.0
C A:ASP185 4.6 14.9 1.0
O A:HOH569 4.6 18.3 1.0
N A:ASP185 4.7 15.1 1.0
CB A:ASP185 4.8 16.9 1.0
C A:ILE188 4.8 12.7 1.0
CB A:GLU177 4.9 12.2 1.0
CA A:ASP185 5.0 13.0 1.0
N A:GLU190 5.0 11.9 1.0

Calcium binding site 3 out of 3 in 5onp

Go back to Calcium Binding Sites List in 5onp
Calcium binding site 3 out of 3 in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd- Substituted 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 Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:16.8
occ:1.00
 O A:ILE197 2.3 19.3 1.0
O A:TYR193 2.3 16.2 1.0
O A:HOH597 2.4 19.8 1.0
OD1 A:ASP200 2.4 18.5 1.0
O A:THR194 2.4 19.1 1.0
OG1 A:THR194 2.4 17.2 1.0
O A:HOH764 2.5 24.7 1.0
C A:THR194 3.2 17.9 1.0
C A:TYR193 3.4 15.2 1.0
CG A:ASP200 3.5 19.2 1.0
CB A:THR194 3.5 18.8 1.0
C A:ILE197 3.5 23.6 1.0
CA A:THR194 3.7 15.4 1.0
OD2 A:ASP200 3.8 20.3 1.0
N A:THR194 3.9 14.9 1.0
CA A:ILE197 4.2 23.0 1.0
CB A:ILE197 4.3 23.4 1.0
N A:ILE197 4.3 24.1 1.0
N A:PRO195 4.3 18.2 1.0
O A:ASP200 4.5 18.6 1.0
N A:SER198 4.5 26.8 1.0
CA A:TYR193 4.6 14.3 1.0
O A:HOH790 4.6 34.3 1.0
O A:GLU190 4.6 15.4 1.0
CD2 A:TYR193 4.6 16.6 1.0
N A:ASP200 4.6 19.5 1.0
CB A:TYR193 4.7 14.8 1.0
CA A:PRO195 4.7 18.9 1.0
CA A:SER198 4.7 28.8 1.0
CB A:ASP200 4.8 20.6 1.0
CG2 A:THR194 4.8 18.1 1.0
C A:ASP200 4.8 16.6 1.0
CG2 A:ILE197 4.9 23.6 1.0
CA A:ASP200 5.0 20.4 1.0
C A:SER198 5.0 27.8 1.0
CG A:TYR193 5.0 16.3 1.0
C A:PRO195 5.0 22.6 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: Sat Dec 12 05:41:32 2020

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