Calcium in PDB 7dt8: Crystal Structure of V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-2-Carboxylic Acid

Protein crystallography data

The structure of Crystal Structure of V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-2-Carboxylic Acid, PDB code: 7dt8 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) 35.50 / 1.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.942, 85.839, 63.282, 90, 90, 90
R / Rfree (%) 16.1 / 17.7

Other elements in 7dt8:

The structure of Crystal Structure of V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-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 V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-2-Carboxylic Acid (pdb code 7dt8). 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 V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-2-Carboxylic Acid, PDB code: 7dt8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7dt8

Go back to Calcium Binding Sites List in 7dt8
Calcium binding site 1 out of 2 in the Crystal Structure of V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-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 V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:41.6
occ:1.00
O A:ASP99 2.4 34.7 1.0
OD1 A:ASP99 2.4 42.1 1.0
OE1 A:GLU66 2.6 29.2 1.0
C A:ASP99 3.4 31.9 1.0
CD A:GLU66 3.5 27.6 1.0
CG A:ASP99 3.6 40.6 1.0
CA A:ASP99 3.8 30.3 1.0
OE2 A:GLU66 3.8 25.7 1.0
O A:HOH357 3.9 38.2 1.0
CB A:ASP99 4.3 34.8 1.0
OD2 A:ASP99 4.5 43.1 1.0
N A:SER100 4.6 31.3 1.0
O A:HOH364 4.6 38.0 1.0
CG A:GLU66 4.6 27.6 1.0
O A:HOH380 4.8 45.2 1.0
O A:ASN98 4.8 25.1 1.0

Calcium binding site 2 out of 2 in 7dt8

Go back to Calcium Binding Sites List in 7dt8
Calcium binding site 2 out of 2 in the Crystal Structure of V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-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 V30M Mutated Transthyretin in Complex with 4- Chloro-9-Oxo-9H-Xanthene-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:70.8
occ:1.00
OE1 B:GLU66 2.8 26.5 1.0
O B:HOH306 2.9 42.4 1.0
OD1 B:ASN98 3.4 42.1 1.0
CD B:GLU66 3.7 23.0 1.0
OE2 B:GLU66 3.7 22.8 1.0
O B:ASP99 4.0 49.0 1.0
N B:ASP99 4.6 37.2 1.0
CG B:ASN98 4.6 40.0 1.0
C B:ASP99 4.8 48.1 1.0
O B:HOH370 4.9 35.9 1.0
CB B:ASP99 4.9 43.0 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 11:35:01 2021

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