Atomistry » Cadmium » PDB 5gu1-5oxd » 5onq
Atomistry »
  Cadmium »
    PDB 5gu1-5oxd »
      5onq »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy