Cadmium in PDB 5onp: 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;

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

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

Calcium

(Ca)

3 atoms

The binding sites of Cadmium 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 Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Alzheimer'S Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd- Substituted Thermolysin, PDB code: 5onp:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 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 Cadmium with other atoms in the Cd 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:Cd404 b:12.6 occ:1.00 NE2 A:HIS142 2.3 12.9 1.0 NE2 A:HIS146 2.3 11.2 1.0 OE2 A:GLU166 2.3 11.9 1.0 O B:ALA30 2.4 17.0 1.0 OE2 A:GLU143 2.6 23.8 1.0 C B:ALA30 3.0 23.1 1.0 CD A:GLU166 3.1 12.0 1.0 CD2 A:HIS142 3.2 10.9 1.0 OE1 A:GLU166 3.3 12.0 1.0 CE1 A:HIS146 3.3 12.2 1.0 CD2 A:HIS146 3.3 10.0 1.0 CE1 A:HIS142 3.3 10.6 1.0 CB B:ALA30 3.5 39.1 1.0 CD A:GLU143 3.6 14.2 1.0 CA B:ALA30 3.6 37.0 1.0 N B:ILE31 3.9 16.7 1.0 OE1 A:GLU143 4.0 20.1 1.0 OH A:TYR157 4.0 14.4 1.0 NE2 A:HIS231 4.2 13.4 1.0 CA B:ILE31 4.2 13.3 1.0 CG A:HIS142 4.4 10.3 1.0 ND1 A:HIS146 4.4 13.6 1.0 ND1 A:HIS142 4.4 10.7 1.0 CG A:HIS146 4.4 12.4 1.0 CG A:GLU166 4.5 12.9 1.0 CB A:SER169 4.8 10.5 1.0 O A:HOH602 4.8 31.9 1.0 CG A:GLU143 4.9 14.4 1.0 C B:ILE31 4.9 13.9 1.0 CD2 A:HIS231 4.9 13.1 1.0 CZ A:TYR157 5.0 13.3 1.0 OG A:SER169 5.0 11.7 1.0

Cadmium binding site 2 out of 2 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 Cadmium with other atoms in the Cd 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:Cd405 b:15.2 occ:1.00 O A:GLN61 2.3 13.0 1.0 OD1 A:ASP57 2.4 13.8 1.0 OD1 A:ASP59 2.4 15.1 1.0 O A:HOH582 2.4 17.1 1.0 O A:HOH788 2.4 16.4 1.0 O A:HOH570 2.5 15.6 1.0 OD2 A:ASP57 2.7 13.6 1.0 CG A:ASP57 2.9 12.5 1.0 CG A:ASP59 3.4 14.4 1.0 C A:GLN61 3.5 11.9 1.0 OD2 A:ASP59 3.7 18.8 1.0 N A:GLN61 3.9 12.2 1.0 O A:HOH694 4.0 18.8 1.0 CA A:GLN61 4.1 12.6 1.0 CB A:GLN61 4.3 15.0 1.0 N A:ASP59 4.3 13.1 1.0 CB A:ASP57 4.3 12.6 1.0 O A:HOH894 4.5 31.2 1.0 O A:HOH876 4.5 18.8 1.0 N A:PHE62 4.6 11.7 1.0 O A:HOH543 4.6 12.4 1.0 CB A:ASP59 4.6 15.0 1.0 OD2 A:ASP67 4.6 13.3 1.0 N A:ALA58 4.7 13.2 1.0 N A:ASN60 4.7 13.2 1.0 CA A:ASP59 4.8 12.9 1.0 CA A:PHE62 4.8 11.4 1.0 C A:ASP59 4.9 13.9 1.0

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