Bromine in PDB 8ii2: Crystal Structure of V30M-Ttr in Complex with Bbm

The structure of Crystal Structure of V30M-Ttr in Complex with Bbm, PDB code: 8ii2 was solved by T.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.57 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.675, 85.109, 64.398, 90, 90, 90
R / Rfree (%)	18.9 / 23.6

The structure of Crystal Structure of V30M-Ttr in Complex with Bbm also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Bromine atom in the Crystal Structure of V30M-Ttr in Complex with Bbm (pdb code 8ii2). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of V30M-Ttr in Complex with Bbm, PDB code: 8ii2:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of V30M-Ttr in Complex with Bbm within 5.0Å range: probe atom residue distance (Å) B Occ A:Br201 b:58.8 occ:0.50 BR1 A:R75201 0.0 58.8 0.5 CAD A:R75201 1.8 44.5 0.5 CAC A:R75201 2.8 44.7 0.5 CAE A:R75201 2.8 40.7 0.5 OAG A:R75201 3.0 46.4 0.5 CD1 A:LEU17 3.5 32.9 1.0 O A:HOH324 3.8 49.8 1.0 CAB A:R75201 4.1 45.7 0.5 CAF A:R75201 4.1 40.4 0.5 NZ A:LYS15 4.3 47.9 1.0 CE A:LYS15 4.6 40.2 1.0 CAA A:R75201 4.6 42.1 0.5 CG A:LEU17 4.6 26.0 1.0 CD2 A:LEU17 4.8 24.7 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of V30M-Ttr in Complex with Bbm within 5.0Å range: probe atom residue distance (Å) B Occ A:Br201 b:59.6 occ:0.50 BR2 A:R75201 0.0 59.6 0.5 CAB A:R75201 1.9 45.7 0.5 CAC A:R75201 2.9 44.7 0.5 CAA A:R75201 2.9 42.1 0.5 OAG A:R75201 3.0 46.4 0.5 CG2 A:THR106 4.1 34.5 1.0 CAD A:R75201 4.2 44.5 0.5 CAF A:R75201 4.2 40.4 0.5 CD A:LYS15 4.5 35.4 1.0 CAE A:R75201 4.7 40.7 0.5 CB A:ALA108 5.0 30.3 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of V30M-Ttr in Complex with Bbm within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:49.6 occ:0.50 BR1 B:R75201 0.0 49.6 0.5 CAD B:R75201 1.9 39.0 0.5 CAE B:R75201 2.8 37.4 0.5 CAC B:R75201 2.8 38.9 0.5 OAG B:R75201 3.0 40.0 0.5 CD1 B:LEU17 3.7 34.7 1.0 CAF B:R75201 4.1 36.7 0.5 CAB B:R75201 4.1 42.6 0.5 O B:HOH335 4.1 51.8 1.0 NZ B:LYS15 4.2 42.7 1.0 CE B:LYS15 4.4 35.8 1.0 CAA B:R75201 4.6 38.5 0.5 CG B:LEU17 4.8 28.4 1.0 CD2 B:LEU17 4.9 26.7 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of V30M-Ttr in Complex with Bbm


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of V30M-Ttr in Complex with Bbm within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:52.8 occ:0.50 BR2 B:R75201 0.0 52.8 0.5 CAB B:R75201 1.9 42.6 0.5 CAC B:R75201 2.9 38.9 0.5 CAA B:R75201 2.9 38.5 0.5 OAG B:R75201 3.1 40.0 0.5 O B:HOH333 3.8 50.5 1.0 CG2 B:THR106 4.0 27.2 1.0 CAD B:R75201 4.2 39.0 0.5 CAF B:R75201 4.3 36.7 0.5 CG2 B:VAL121 4.4 30.9 1.0 CD B:LYS15 4.5 32.1 1.0 CB B:THR106 4.8 29.0 1.0 CAE B:R75201 4.8 37.4 0.5 CB B:VAL121 5.0 28.0 1.0

M.Mizuguchi, T.Yokoyama, T.Okada, Y.Nakagawa, K.Fujii, Y.Nabeshima, N.Toyooka. Benziodarone and 6-Hydroxybenziodarone Are Potent and Selective Inhibitors of Transthyretin Amyloidogenesis. Bioorg.Med.Chem. V. 90 17370 2023.
ISSN: ESSN 1464-3391
PubMed: 37311373
DOI: 10.1016/J.BMC.2023.117370