Bromine in PDB 4y9c: Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin

The structure of Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin, PDB code: 4y9c was solved by T.Yokoyama, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.54 / 1.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.089, 85.624, 63.552, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24

The binding sites of Bromine atom in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin (pdb code 4y9c). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin, PDB code: 4y9c:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin


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 Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:42.7 occ:0.50 NZ A:LYS15 3.9 42.2 1.0 CE A:LYS15 3.9 32.9 1.0 CAM A:MKS201 4.1 21.0 0.5 CD1 A:LEU17 4.4 13.1 1.0 OAQ A:MKS201 4.8 20.2 0.5 OAH A:MKS201 4.8 21.6 0.5 CAU A:MKS201 4.9 21.1 0.5 CBB A:MKS201 5.0 21.3 0.5

Bromine binding site 2 out of 6 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin


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 Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br203 b:39.9 occ:0.80 O B:HOH359 2.8 35.9 1.0 NZ A:LYS35 3.1 32.9 1.0 CE1 B:HIS90 3.7 29.6 1.0 CE A:LYS35 3.8 35.9 1.0 O B:HOH303 4.0 36.2 1.0 CZ2 A:TRP41 4.0 20.1 1.0 CG2 A:ILE68 4.0 14.1 1.0 CG1 A:VAL94 4.0 13.7 1.0 CD A:LYS35 4.1 34.0 1.0 ND1 B:HIS90 4.2 25.9 1.0 CH2 A:TRP41 4.2 18.2 1.0 CB B:GLU89 4.4 16.2 1.0 CD1 A:ILE68 4.5 16.1 1.0 CG B:GLU89 4.5 18.9 1.0 NE2 B:HIS90 4.8 28.6 1.0 OE1 B:GLU89 4.9 22.4 1.0

Bromine binding site 3 out of 6 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin


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 Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br204 b:42.3 occ:0.50 O A:HOH302 3.3 25.7 1.0 NE2 A:HIS31 3.6 17.8 1.0 CD2 A:HIS31 3.7 16.2 1.0 CE1 A:HIS31 3.7 17.1 1.0 ND1 A:HIS31 3.7 17.7 1.0 O A:HOH344 3.7 35.3 1.0 CG A:HIS31 3.7 14.8 1.0 OE1 A:GLU72 4.4 25.1 1.0 CB A:HIS31 4.5 12.7 1.0 O A:HOH310 4.7 24.8 1.0 CZ A:PHE33 4.8 16.7 1.0

Bromine binding site 4 out of 6 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin


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 Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br205 b:38.2 occ:0.30 N A:GLU51 3.7 19.7 1.0 CB A:SER50 3.9 16.9 1.0 CG A:GLU51 4.1 37.8 1.0 CA A:SER50 4.2 17.4 1.0 CB A:GLU51 4.4 28.2 1.0 C A:SER50 4.5 17.6 1.0 CD A:GLU51 4.7 47.8 1.0 CA A:GLU51 4.7 21.1 1.0 OE2 A:GLU51 4.8 51.5 1.0

Bromine binding site 5 out of 6 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:36.9 occ:0.80 O A:HOH305 2.9 42.0 1.0 CE B:LYS35 3.4 41.7 1.0 NZ B:LYS35 3.7 44.8 1.0 CE1 A:HIS90 3.7 25.3 1.0 CG2 B:ILE68 4.0 15.3 1.0 CG1 B:VAL94 4.0 16.1 1.0 CZ2 B:TRP41 4.1 23.4 1.0 CH2 B:TRP41 4.1 19.9 1.0 ND1 A:HIS90 4.2 23.1 1.0 CB A:GLU89 4.3 18.2 1.0 CG A:GLU89 4.3 18.7 1.0 CD1 B:ILE68 4.5 20.4 1.0 OE1 A:GLU89 4.8 27.1 1.0 CD B:LYS35 4.8 36.8 1.0 NE2 A:HIS90 4.8 30.7 1.0

Bromine binding site 6 out of 6 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Alpha-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br203 b:36.6 occ:0.50 CAM B:MKS202 3.9 19.9 0.5 CG2 B:VAL121 4.1 21.2 1.0 CG2 B:THR106 4.1 18.1 1.0 CB B:VAL121 4.2 19.9 1.0 CB B:THR106 4.4 18.5 1.0 OAQ B:MKS202 4.4 23.1 0.5 CG1 B:VAL121 4.5 22.5 1.0 OG1 B:THR106 4.7 21.9 1.0 OAH B:MKS202 4.7 18.1 0.5 CBB B:MKS202 4.7 21.3 0.5 CAU B:MKS202 4.8 20.8 0.5

T.Yokoyama, M.Ueda, Y.Ando, M.Mizuguchi. Discovery of Gamma-Mangostin As An Amyloidogenesis Inhibitor Sci Rep V. 5 13570 2015.
ISSN: ESSN 2045-2322
PubMed: 26310724
DOI: 10.1038/SREP13570