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Cadmium in PDB 5onq: Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin

Enzymatic activity of Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin

All present enzymatic activity of Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin, PDB code: 5onq 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) 43.97 / 1.17
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.488, 93.488, 129.558, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 17.2

Other elements in 5onq:

The structure of Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin (pdb code 5onq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin, PDB code: 5onq:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 5onq

Go back to Cadmium Binding Sites List in 5onq
Cadmium binding site 1 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 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 29-40 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:9.4
occ:1.00
 NE2 A:HIS142 2.3 9.6 1.0
OE1 A:GLU166 2.3 10.4 1.0
NE2 A:HIS146 2.3 8.9 1.0
O B:ALA30 2.4 11.7 1.0
OE2 A:GLU143 2.6 18.3 1.0
C B:ALA30 3.0 15.7 1.0
CD A:GLU166 3.1 9.3 1.0
OE2 A:GLU166 3.2 10.8 1.0
CD2 A:HIS142 3.2 9.1 1.0
CE1 A:HIS146 3.3 9.6 1.0
CD2 A:HIS146 3.3 8.7 1.0
CE1 A:HIS142 3.3 9.1 1.0
CB B:ALA30 3.5 30.6 1.0
CA B:ALA30 3.6 26.2 1.0
CD A:GLU143 3.6 12.8 1.0
N B:ILE31 3.9 13.1 1.0
OE1 A:GLU143 4.0 14.8 1.0
OH A:TYR157 4.1 11.2 1.0
CA B:ILE31 4.2 11.3 1.0
NE2 A:HIS231 4.2 10.3 1.0
CG A:HIS142 4.4 8.6 1.0
ND1 A:HIS146 4.4 9.3 1.0
ND1 A:HIS142 4.4 8.9 1.0
CG A:HIS146 4.5 9.1 1.0
CG A:GLU166 4.5 9.9 1.0
O A:HOH623 4.6 18.9 1.0
CB A:SER169 4.8 7.5 1.0
CG A:GLU143 4.9 13.8 1.0
C B:ILE31 4.9 10.6 1.0
CD2 A:HIS231 4.9 10.8 1.0
OG A:SER169 5.0 9.1 1.0

Cadmium binding site 2 out of 4 in 5onq

Go back to Cadmium Binding Sites List in 5onq
Cadmium binding site 2 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 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 29-40 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:13.1
occ:1.00
 OE2 A:GLU190 2.3 12.4 1.0
O A:ASN183 2.4 15.8 1.0
OD2 A:ASP185 2.4 14.7 1.0
O A:HOH533 2.4 14.5 1.0
OE1 A:GLU177 2.4 11.8 1.0
O A:HOH528 2.4 16.3 1.0
CD A:GLU177 3.2 9.5 1.0
CG A:ASP185 3.2 12.3 1.0
CD A:GLU190 3.3 10.7 1.0
C A:ASN183 3.5 14.8 1.0
OD1 A:ASP185 3.5 11.6 1.0
OE2 A:GLU177 3.6 11.1 1.0
CD A:CD404 3.7 13.3 1.0
CG A:GLU190 3.8 12.3 1.0
O A:HOH555 4.1 30.7 1.0
N A:ASP185 4.1 12.8 1.0
CA A:PRO184 4.1 12.7 1.0
OD1 A:ASP191 4.1 14.8 1.0
CB A:ASN183 4.2 18.1 1.0
OD2 A:ASP191 4.2 15.5 1.0
CG A:GLU177 4.2 10.7 1.0
OE1 A:GLU190 4.2 10.8 1.0
C A:PRO184 4.2 12.6 1.0
N A:PRO184 4.3 14.1 1.0
CB A:ASP185 4.3 12.8 1.0
O A:LYS182 4.3 17.9 1.0
O A:HOH539 4.4 19.1 1.0
O A:HOH831 4.4 25.8 1.0
CA A:ASN183 4.5 18.4 1.0
CG A:ASP191 4.5 12.3 1.0
CA A:ASP185 4.8 11.3 1.0
O A:PRO184 4.9 14.4 1.0
O A:HOH729 5.0 31.6 1.0

Cadmium binding site 3 out of 4 in 5onq

Go back to Cadmium Binding Sites List in 5onq
Cadmium binding site 3 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 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 3 of Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:13.3
occ:1.00
 OD2 A:ASP138 2.4 10.1 1.0
O A:GLU187 2.4 10.7 1.0
OE2 A:GLU177 2.4 11.1 1.0
O A:HOH574 2.5 11.0 1.0
OD1 A:ASP185 2.5 11.6 1.0
OE2 A:GLU190 2.5 12.4 1.0
OE1 A:GLU190 2.5 10.8 1.0
CD A:GLU190 2.9 10.7 1.0
OE1 A:GLU177 2.9 11.8 1.0
CD A:GLU177 3.0 9.5 1.0
CG A:ASP138 3.3 9.7 1.0
C A:GLU187 3.4 11.0 1.0
CG A:ASP185 3.5 12.3 1.0
CD A:CD403 3.7 13.1 1.0
OD2 A:ASP185 3.9 14.7 1.0
CB A:ASP138 3.9 9.4 1.0
O A:HOH539 4.1 19.1 1.0
O A:ASP185 4.2 11.7 1.0
N A:ILE188 4.2 10.7 1.0
N A:GLU187 4.2 10.9 1.0
OD1 A:ASP138 4.2 12.0 1.0
CA A:ILE188 4.3 10.4 1.0
CA A:GLU187 4.3 11.9 1.0
CG A:GLU190 4.3 12.3 1.0
N A:GLY189 4.4 9.8 1.0
O A:HOH562 4.4 14.9 1.0
CG A:GLU177 4.4 10.7 1.0
CB A:GLU187 4.6 12.6 1.0
C A:ASP185 4.6 12.9 1.0
C A:ILE188 4.7 10.4 1.0
CB A:ASP185 4.8 12.8 1.0
N A:ASP185 4.8 12.8 1.0
O A:HOH533 4.9 14.5 1.0
CB A:GLU177 4.9 10.1 1.0
N A:GLU190 4.9 10.4 1.0

Cadmium binding site 4 out of 4 in 5onq

Go back to Cadmium Binding Sites List in 5onq
Cadmium binding site 4 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 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 4 of Alzheimer'S Amyloid-Beta Peptide Fragment 29-40 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:10.2
occ:1.00
 O A:GLN61 2.3 11.0 1.0
OD1 A:ASP57 2.3 8.9 1.0
O A:HOH779 2.4 12.8 1.0
OD1 A:ASP59 2.4 10.8 1.0
O A:HOH538 2.4 11.1 1.0
O A:HOH586 2.5 11.9 1.0
OD2 A:ASP57 2.7 10.7 1.0
CG A:ASP57 2.9 9.5 1.0
CG A:ASP59 3.3 10.5 1.0
C A:GLN61 3.4 9.3 1.0
OD2 A:ASP59 3.6 14.2 1.0
N A:GLN61 3.9 9.6 1.0
O A:HOH700 4.0 14.3 1.0
CA A:GLN61 4.1 10.4 1.0
CB A:GLN61 4.2 11.3 1.0
N A:ASP59 4.3 9.5 1.0
CB A:ASP57 4.3 9.5 1.0
O A:HOH848 4.5 15.7 1.0
N A:PHE62 4.5 8.3 1.0
O A:HOH866 4.5 24.5 1.0
O A:HOH535 4.5 9.6 1.0
CB A:ASP59 4.6 10.5 1.0
OD2 A:ASP67 4.6 10.0 1.0
N A:ALA58 4.7 9.5 1.0
N A:ASN60 4.7 9.4 1.0
CA A:PHE62 4.8 8.8 1.0
CA A:ASP59 4.8 10.6 1.0
C A:ASP59 4.9 9.6 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: Fri Jul 19 18:42:27 2024

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