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

Go back to Calcium Binding Sites List in 6ghx
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

Go back to Calcium Binding Sites List in 6ghx
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

Go back to Calcium Binding Sites List in 6ghx
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: Sat Dec 12 06:08:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy