Calcium in PDB 7ejq: Crystal Structure of Human Transthyretin in Complex with 8-Chloro-9- Oxo-9H-Xanthene-3-Carboxylic Acid

Protein crystallography data

The structure of Crystal Structure of Human Transthyretin in Complex with 8-Chloro-9- Oxo-9H-Xanthene-3-Carboxylic Acid, PDB code: 7ejq 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) 29.95 / 1.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.027, 85.359, 63.487, 90, 90, 90
R / Rfree (%) 14.5 / 16.7

Other elements in 7ejq:

The structure of Crystal Structure of Human Transthyretin in Complex with 8-Chloro-9- Oxo-9H-Xanthene-3-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 8-Chloro-9- Oxo-9H-Xanthene-3-Carboxylic Acid (pdb code 7ejq). 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 8-Chloro-9- Oxo-9H-Xanthene-3-Carboxylic Acid, PDB code: 7ejq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7ejq

Go back to Calcium Binding Sites List in 7ejq
Calcium binding site 1 out of 2 in the Crystal Structure of Human Transthyretin in Complex with 8-Chloro-9- Oxo-9H-Xanthene-3-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 8-Chloro-9- Oxo-9H-Xanthene-3-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:27.3
occ:1.00
OD1 A:ASP99 2.3 30.0 1.0
O A:HOH381 2.3 31.3 1.0
OE1 A:GLU66 2.5 17.9 1.0
O A:ASP99 2.6 20.3 1.0
HA A:ASP99 3.2 24.1 1.0
CD A:GLU66 3.3 15.9 1.0
CG A:ASP99 3.5 29.9 1.0
C A:ASP99 3.5 20.7 1.0
OE2 A:GLU66 3.6 16.2 1.0
CA A:ASP99 3.8 20.1 1.0
O A:HOH367 3.8 27.5 1.0
O A:HOH348 3.9 25.9 1.0
CB A:ASP99 4.2 24.6 1.0
OD2 A:ASP99 4.4 32.5 1.0
O A:HOH376 4.5 39.4 1.0
O A:HOH357 4.6 20.1 1.0
CG A:GLU66 4.6 16.2 1.0
HG2 A:GLU66 4.6 19.5 1.0
HB3 A:ASP99 4.7 29.5 1.0
HA A:SER100 4.7 30.4 1.0
N A:SER100 4.7 22.4 1.0
O A:ASN98 4.9 15.7 1.0
HB2 A:ASP99 5.0 29.5 1.0

Calcium binding site 2 out of 2 in 7ejq

Go back to Calcium Binding Sites List in 7ejq
Calcium binding site 2 out of 2 in the Crystal Structure of Human Transthyretin in Complex with 8-Chloro-9- Oxo-9H-Xanthene-3-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 8-Chloro-9- Oxo-9H-Xanthene-3-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:22.8
occ:1.00
O B:HOH339 2.3 23.1 1.0
OD1 B:ASN98 2.4 23.0 1.0
OE1 B:GLU66 2.6 16.2 1.0
CD B:GLU66 3.5 14.2 1.0
CG B:ASN98 3.6 23.2 1.0
OE2 B:GLU66 3.8 14.2 1.0
H B:ASP99 3.9 21.5 1.0
HD22 B:ASN98 4.1 31.5 1.0
HA B:ASN98 4.2 19.7 1.0
ND2 B:ASN98 4.3 26.2 1.0
O B:HOH341 4.3 23.3 1.0
N B:ASP99 4.5 17.9 1.0
HB2 B:ASP99 4.6 22.7 1.0
CB B:ASN98 4.7 19.2 1.0
CA B:ASN98 4.8 16.4 1.0
CG B:GLU66 4.9 13.2 1.0
HG2 B:GLU66 4.9 15.9 1.0
HB2 B:ASN98 4.9 23.1 1.0
O B:ASP99 5.0 27.6 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 Nov 5 11:35:30 2021

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