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

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

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

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 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 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

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