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Calcium in PDB 6ghx: Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd- Substituted Thermolysin

Enzymatic activity of Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd- Substituted Thermolysin

All present enzymatic activity of Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd- Substituted Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd- Substituted Thermolysin, PDB code: 6ghx 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) 46.53 / 1.16
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.060, 93.060, 130.290, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 22

Other elements in 6ghx:

The structure of Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd- Substituted Thermolysin also contains other interesting chemical elements:

Cadmium (Cd) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd- Substituted Thermolysin (pdb code 6ghx). 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 31-35 in Complex with Cd- Substituted Thermolysin, PDB code: 6ghx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ghx

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Calcium binding site 1 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 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 31-35 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:11.0
occ:1.00
 O A:HOH733 2.2 20.2 1.0
O A:GLN61 2.2 17.6 1.0
O A:HOH647 2.3 20.1 1.0
OD1 A:ASP59 2.4 17.3 1.0
OD1 A:ASP57 2.4 12.2 1.0
O A:HOH511 2.4 14.0 1.0
OD2 A:ASP57 2.6 17.7 1.0
CG A:ASP57 2.8 15.4 1.0
CG A:ASP59 3.3 19.5 1.0
C A:GLN61 3.4 16.8 1.0
OD2 A:ASP59 3.7 22.1 1.0
N A:GLN61 3.9 18.2 1.0
O A:HOH670 4.0 23.4 1.0
CA A:GLN61 4.0 19.0 1.0
CB A:GLN61 4.1 18.8 1.0
CB A:ASP57 4.3 16.7 1.0
N A:ASP59 4.3 19.2 1.0
N A:PHE62 4.5 17.2 1.0
O A:HOH840 4.5 32.9 1.0
O A:HOH822 4.6 28.1 1.0
O A:HOH533 4.6 19.8 1.0
CB A:ASP59 4.6 19.3 1.0
OD2 A:ASP67 4.6 18.0 1.0
N A:ALA58 4.7 18.4 1.0
N A:ASN60 4.7 18.1 1.0
CA A:PHE62 4.8 17.7 1.0
CA A:ASP59 4.8 17.9 1.0
C A:ASP59 4.9 18.3 1.0

Calcium binding site 2 out of 4 in 6ghx

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Calcium binding site 2 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 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 31-35 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:12.5
occ:1.00
 O A:GLU187 2.3 18.8 1.0
OD2 A:ASP138 2.3 19.3 1.0
OE1 A:GLU177 2.4 20.3 1.0
O A:HOH562 2.5 20.9 1.0
OD1 A:ASP185 2.5 18.5 1.0
OE1 A:GLU190 2.5 17.8 1.0
OE2 A:GLU190 2.5 19.8 1.0
OE2 A:GLU177 2.8 19.8 1.0
CD A:GLU190 2.8 19.1 1.0
CD A:GLU177 2.9 18.5 1.0
CG A:ASP138 3.3 19.2 1.0
C A:GLU187 3.3 19.1 1.0
CG A:ASP185 3.5 21.2 1.0
CA A:CA403 3.8 12.5 1.0
OD2 A:ASP185 3.9 21.5 1.0
CB A:ASP138 3.9 16.9 1.0
O A:HOH574 4.2 31.8 1.0
O A:ASP185 4.2 20.3 1.0
N A:ILE188 4.2 20.4 1.0
N A:GLU187 4.2 20.6 1.0
OD1 A:ASP138 4.2 21.2 1.0
CA A:GLU187 4.3 19.8 1.0
CA A:ILE188 4.3 18.8 1.0
CG A:GLU190 4.3 18.1 1.0
N A:GLY189 4.4 17.6 1.0
CG A:GLU177 4.4 19.3 1.0
O A:HOH563 4.5 23.1 1.0
CB A:GLU187 4.6 20.8 1.0
C A:ASP185 4.6 20.9 1.0
C A:ILE188 4.7 18.6 1.0
CB A:ASP185 4.8 19.4 1.0
N A:ASP185 4.8 20.6 1.0
O A:HOH560 4.8 24.3 1.0
CB A:GLU177 4.9 18.2 1.0
N A:GLU190 4.9 18.6 1.0
OG1 A:THR174 4.9 18.6 1.0

Calcium binding site 3 out of 4 in 6ghx

Go back to Calcium Binding Sites List in 6ghx
Calcium binding site 3 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 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 31-35 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.5
occ:1.00
 OE2 A:GLU190 2.3 19.8 1.0
OD2 A:ASP185 2.3 21.5 1.0
O A:HOH560 2.3 24.3 1.0
O A:ASN183 2.4 25.0 1.0
OE2 A:GLU177 2.4 19.8 1.0
O A:HOH685 2.5 21.8 1.0
CD A:GLU177 3.1 18.5 1.0
CG A:ASP185 3.1 21.2 1.0
CD A:GLU190 3.2 19.1 1.0
OD1 A:ASP185 3.5 18.5 1.0
C A:ASN183 3.5 24.4 1.0
OE1 A:GLU177 3.6 20.3 1.0
CG A:GLU190 3.7 18.1 1.0
CA A:CA402 3.8 12.5 1.0
N A:ASP185 4.1 20.6 1.0
CA A:PRO184 4.1 24.7 1.0
O A:HOH573 4.2 52.6 1.0
CG A:GLU177 4.2 19.3 1.0
OD2 A:ASP191 4.2 26.7 1.0
CB A:ASN183 4.2 25.4 1.0
OD1 A:ASP191 4.2 24.3 1.0
OE1 A:GLU190 4.2 17.8 1.0
C A:PRO184 4.2 22.3 1.0
O A:HOH790 4.3 46.6 1.0
O A:HOH574 4.3 31.8 1.0
N A:PRO184 4.3 24.8 1.0
CB A:ASP185 4.3 19.4 1.0
O A:LYS182 4.4 24.9 1.0
CA A:ASN183 4.5 28.2 1.0
CG A:ASP191 4.5 23.8 1.0
CA A:ASP185 4.8 20.4 1.0
O A:PRO184 4.9 24.0 1.0

Calcium binding site 4 out of 4 in 6ghx

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Calcium binding site 4 out of 4 in the Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 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 4 of Alzheimer'S Amyloid-Beta Peptide Fragment 31-35 in Complex with Cd- Substituted Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:23.0
occ:1.00
 O A:ILE197 2.3 26.1 1.0
O A:TYR193 2.4 21.6 1.0
OD1 A:ASP200 2.4 24.5 1.0
O A:HOH582 2.4 24.6 1.0
OG1 A:THR194 2.4 24.4 1.0
O A:THR194 2.4 24.7 1.0
O A:HOH725 2.5 32.0 1.0
C A:THR194 3.2 23.5 1.0
C A:TYR193 3.3 21.5 1.0
CG A:ASP200 3.4 26.5 1.0
C A:ILE197 3.5 28.4 1.0
CB A:THR194 3.5 24.5 1.0
CA A:THR194 3.7 21.9 1.0
OD2 A:ASP200 3.8 26.2 1.0
N A:THR194 3.9 21.4 1.0
CA A:ILE197 4.2 25.9 1.0
N A:ILE197 4.3 28.6 1.0
CB A:ILE197 4.3 28.1 1.0
N A:PRO195 4.3 26.5 1.0
O A:ASP200 4.5 24.0 1.0
N A:SER198 4.5 34.6 1.0
CA A:TYR193 4.5 20.9 1.0
CD2 A:TYR193 4.6 22.6 1.0
N A:ASP200 4.6 27.8 1.0
CB A:TYR193 4.6 21.4 1.0
O A:GLU190 4.7 20.8 1.0
CA A:SER198 4.7 34.8 1.0
CA A:PRO195 4.7 25.0 1.0
O A:HOH761 4.7 33.2 1.0
CB A:ASP200 4.7 23.2 1.0
CG2 A:THR194 4.7 25.0 1.0
C A:ASP200 4.8 23.4 1.0
CG2 A:ILE197 4.9 28.4 1.0
CG A:TYR193 4.9 23.6 1.0
CA A:ASP200 4.9 25.0 1.0
C A:PRO195 5.0 27.7 1.0
C A:SER198 5.0 32.5 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: Tue Jul 16 08:05:18 2024

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