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Chlorine in PDB 7dt5: Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9- Oxo-9H-Xanthene-2-Carboxylic Acid

Protein crystallography data

The structure of Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9- Oxo-9H-Xanthene-2-Carboxylic Acid, PDB code: 7dt5 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) 30.09 / 1.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.205, 85.797, 63.773, 90, 90, 90
R / Rfree (%) 16.2 / 18.5

Other elements in 7dt5:

The structure of Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9- Oxo-9H-Xanthene-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- Oxo-9H-Xanthene-2-Carboxylic Acid (pdb code 7dt5). 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- Oxo-9H-Xanthene-2-Carboxylic Acid, PDB code: 7dt5:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7dt5

Go back to Chlorine Binding Sites List in 7dt5
Chlorine binding site 1 out of 2 in the Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9- Oxo-9H-Xanthene-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- Oxo-9H-Xanthene-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:23.7
occ:0.50
CL1 A:HH9202 0.0 23.7 0.5
CAM A:HH9202 1.8 21.8 0.5
CAJ A:HH9202 2.8 21.8 0.5
CAN A:HH9202 2.8 22.4 0.5
OAI A:HH9202 2.9 20.6 0.5
CB A:ALA108 3.4 17.8 1.0
CG2 A:VAL121 3.4 20.9 1.0
O A:THR119 3.7 15.5 1.0
CG2 A:THR119 3.9 20.0 1.0
CB A:THR119 4.0 17.8 1.0
O A:THR106 4.0 15.0 1.0
CAL A:HH9202 4.1 22.2 0.5
CAH A:HH9202 4.1 23.7 0.5
N A:ALA108 4.1 13.2 1.0
N A:VAL121 4.1 12.8 1.0
C A:THR119 4.1 13.4 1.0
CB A:VAL121 4.1 17.7 1.0
CAB A:HH9202 4.3 22.2 0.5
CA A:ALA108 4.3 14.4 1.0
C A:ALA120 4.4 12.8 1.0
CG2 A:THR106 4.4 17.9 1.0
N A:ALA120 4.6 13.0 1.0
CAK A:HH9202 4.6 22.6 0.5
CA A:ALA120 4.7 13.3 1.0
CA A:THR119 4.7 14.3 1.0
CA A:VAL121 4.7 14.3 1.0
C A:THR106 4.8 13.1 1.0
C A:ILE107 4.9 13.0 1.0
CB A:THR106 4.9 16.4 1.0

Chlorine binding site 2 out of 2 in 7dt5

Go back to Chlorine Binding Sites List in 7dt5
Chlorine binding site 2 out of 2 in the Crystal Structure of Human Transthyretin in Complex with 4-Chloro-9- Oxo-9H-Xanthene-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- Oxo-9H-Xanthene-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:25.5
occ:0.50
CL1 B:HH9202 0.0 25.5 0.5
CAM B:HH9202 1.8 23.6 0.5
CAJ B:HH9202 2.7 24.1 0.5
CAN B:HH9202 2.7 26.0 0.5
OAI B:HH9202 2.9 23.9 0.5
OG1 B:THR119 2.9 26.8 0.5
CB B:ALA108 3.2 17.9 1.0
CG2 B:VAL121 3.2 25.7 1.0
O B:THR119 3.8 14.8 1.0
CB B:VAL121 3.9 21.7 1.0
CAL B:HH9202 4.0 24.3 0.5
CAH B:HH9202 4.0 24.5 0.5
N B:ALA108 4.1 13.9 1.0
N B:VAL121 4.2 14.2 1.0
CA B:ALA108 4.2 14.2 1.0
O B:THR106 4.2 15.7 1.0
CB B:THR119 4.2 15.8 0.5
C B:THR119 4.3 13.8 1.0
CAB B:HH9202 4.3 23.6 0.5
CB B:THR119 4.3 22.3 0.5
CG2 B:THR106 4.4 19.4 1.0
CAK B:HH9202 4.6 24.6 0.5
CG2 B:THR119 4.6 15.9 0.5
C B:ALA120 4.6 14.2 1.0
CA B:VAL121 4.7 17.0 1.0
N B:ALA120 4.8 13.8 1.0
CG2 B:THR119 4.8 22.8 0.5
CA B:THR119 4.8 13.7 0.5
CA B:THR119 4.9 16.2 0.5
C B:THR106 4.9 13.7 1.0
CB B:THR106 4.9 17.8 1.0
CA B:ALA120 4.9 14.6 1.0
C B:ILE107 5.0 13.5 1.0
CAD B:HH9202 5.0 23.6 0.5

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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