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Calcium in PDB 7dt3: Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid

Protein crystallography data

The structure of Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid, PDB code: 7dt3 was solved by R.Kitakami, T.Yokoyama, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.85 / 1.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.029, 85.773, 63.708, 90, 90, 90
R / Rfree (%) 16.6 / 18.7

Other elements in 7dt3:

The structure of Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid (pdb code 7dt3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid, PDB code: 7dt3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7dt3

Go back to Calcium Binding Sites List in 7dt3
Calcium binding site 1 out of 2 in the Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:27.6
occ:1.00
O A:HOH379 2.3 34.2 1.0
OD1 A:ASP99 2.3 30.8 1.0
OE1 A:GLU66 2.4 23.2 1.0
O A:ASP99 2.6 22.4 1.0
CD A:GLU66 3.3 20.4 1.0
OE2 A:GLU66 3.5 20.0 1.0
CG A:ASP99 3.6 31.1 1.0
C A:ASP99 3.6 21.8 1.0
CA A:ASP99 3.8 21.7 1.0
O A:HOH347 3.9 31.6 1.0
O A:HOH318 4.1 27.5 1.0
CB A:ASP99 4.3 25.6 1.0
OD2 A:ASP99 4.5 34.2 1.0
CG A:GLU66 4.6 19.5 1.0
O A:HOH368 4.6 21.3 1.0
N A:SER100 4.8 24.0 1.0
O A:ASN98 4.8 18.2 1.0

Calcium binding site 2 out of 2 in 7dt3

Go back to Calcium Binding Sites List in 7dt3
Calcium binding site 2 out of 2 in the Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9, 10-Dioxo-9,10-Dihydroanthracene-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:33.9
occ:1.00
ND2 B:ASN98 2.3 32.9 1.0
OE1 B:GLU66 2.6 18.9 1.0
CG B:ASN98 3.5 31.6 1.0
CD B:GLU66 3.5 17.0 1.0
OE2 B:GLU66 3.8 17.0 1.0
OD1 B:ASN98 4.1 35.0 1.0
O B:HOH355 4.3 26.5 1.0
N B:ASP99 4.5 20.5 1.0
CB B:ASN98 4.6 25.7 1.0
CA B:ASN98 4.8 20.5 1.0
CG B:GLU66 4.9 15.8 1.0
O B:ASP99 5.0 31.2 1.0

Reference:

R.Kitakami, K.Inui, Y.Nakagawa, Y.Sawai, W.Katayama, T.Yokoyama, T.Okada, K.Kanamitsu, S.Nakagawa, N.Toyooka, M.Mizuguchi. Inhibitory Activities of Anthraquinone and Xanthone Derivatives Against Transthyretin Amyloidogenesis. Bioorg.Med.Chem. V. 44 16292 2021.
ISSN: ESSN 1464-3391
PubMed: 34225167
DOI: 10.1016/J.BMC.2021.116292
Page generated: Fri Jul 19 00:09:54 2024

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