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Chlorine 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:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7dt3

Go back to Chlorine Binding Sites List in 7dt3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl202

b:22.9
occ:0.50
CL1 A:HG6202 0.0 22.9 0.5
CAM A:HG6202 1.8 25.3 0.5
CAN A:HG6202 2.7 24.1 0.5
OAT A:HG6202 2.7 22.4 0.5
CAJ A:HG6202 2.8 22.6 0.5
CAI A:HG6202 3.1 23.3 0.5
CAL A:HG6202 4.0 30.7 0.5
CAH A:HG6202 4.1 22.9 0.5
CAB A:HG6202 4.5 20.5 0.5
CAK A:HG6202 4.5 28.7 0.5

Chlorine binding site 2 out of 2 in 7dt3

Go back to Chlorine Binding Sites List in 7dt3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl202

b:22.9
occ:0.50
CL1 B:HG6202 0.0 22.9 0.5
CAM B:HG6202 1.7 25.3 0.5
CAN B:HG6202 2.7 24.1 0.5
OAT B:HG6202 2.7 22.4 0.5
CAJ B:HG6202 2.7 22.6 0.5
CAI B:HG6202 3.1 23.3 0.5
O B:ALA109 3.2 14.2 1.0
O B:LYS15 3.3 13.6 1.0
N B:ALA109 3.5 11.7 1.0
CG B:LEU17 3.5 15.7 1.0
CB B:ALA108 3.5 15.4 1.0
C B:LYS15 3.8 12.0 1.0
C B:ALA109 3.8 11.7 1.0
CD1 B:LEU17 3.8 17.8 1.0
N B:LEU17 3.9 12.3 1.0
CA B:ALA108 3.9 12.6 1.0
CAL B:HG6202 4.0 30.7 0.5
CAH B:HG6202 4.0 22.9 0.5
C B:ALA108 4.0 13.0 1.0
N B:VAL16 4.1 11.9 1.0
CB B:LEU17 4.1 13.3 1.0
CA B:VAL16 4.1 11.8 1.0
CB B:LYS15 4.1 14.9 1.0
C B:VAL16 4.2 12.2 1.0
CA B:ALA109 4.3 11.8 1.0
CAB B:HG6202 4.5 20.5 0.5
CAK B:HG6202 4.5 28.7 0.5
CD2 B:LEU17 4.6 17.6 1.0
CA B:LYS15 4.6 13.0 1.0
N B:LEU110 4.6 10.6 1.0
CA B:LEU17 4.6 11.5 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: Mon Jul 29 20:18:34 2024

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