Bromine in PDB 4y9f: Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin

The structure of Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin, PDB code: 4y9f 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)	28.55 / 1.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.043, 85.638, 63.391, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.1

The binding sites of Bromine atom in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin (pdb code 4y9f). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin, PDB code: 4y9f:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-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 Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br202 b:34.1 occ:0.50 OAH A:MKT201 2.9 17.9 0.5 CAC A:MKT201 3.5 14.5 0.5 CAU A:MKT201 4.0 16.5 0.5 CAO A:MKT201 4.2 14.8 0.5 CAX A:MKT201 4.5 16.2 0.5 CD2 A:LEU110 4.6 12.2 1.0 CAR A:MKT201 4.7 14.2 0.5 CAS A:MKT201 4.9 17.1 0.5 OAF A:MKT201 4.9 16.3 0.5 CAK A:MKT201 5.0 14.9 0.5

Bromine binding site 2 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-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 Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br203 b:46.2 occ:0.50 CAL A:MKT201 4.0 18.1 0.5 CE A:LYS15 4.0 26.8 1.0 NZ A:LYS15 4.1 37.5 1.0 CD1 A:LEU17 4.4 12.8 1.0 OAP A:MKT201 4.6 18.1 0.5 OAF A:MKT201 4.8 16.3 0.5 CAS A:MKT201 4.9 17.1 0.5 CBA A:MKT201 4.9 17.9 0.5

Bromine binding site 3 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-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 Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br204 b:38.0 occ:0.50 O A:HOH312 3.1 25.7 1.0 NE2 A:HIS31 3.6 18.2 1.0 CD2 A:HIS31 3.6 16.3 1.0 CE1 A:HIS31 3.7 16.1 1.0 ND1 A:HIS31 3.7 17.7 1.0 CG A:HIS31 3.7 14.2 1.0 O A:HOH342 3.7 29.5 1.0 CB A:HIS31 4.4 11.7 1.0 OE1 A:GLU72 4.5 21.0 1.0 O A:HOH314 4.8 23.1 1.0 CZ A:PHE33 4.8 15.7 1.0

Bromine binding site 4 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-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 Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br205 b:37.3 occ:0.30 N A:GLU51 3.6 16.8 1.0 CB A:SER50 3.7 13.9 1.0 CG A:GLU51 3.9 31.4 1.0 CA A:SER50 4.0 13.9 1.0 CB A:GLU51 4.1 23.1 1.0 C A:SER50 4.3 15.6 1.0 CD A:GLU51 4.5 39.5 1.0 CA A:GLU51 4.5 18.4 1.0 OE2 A:GLU51 4.7 42.0 1.0 OG A:SER50 4.8 16.2 1.0

Bromine binding site 5 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-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 Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br206 b:36.1 occ:0.80 O B:HOH359 3.1 34.1 1.0 NZ A:LYS35 3.3 33.9 1.0 CE1 B:HIS90 3.6 24.6 1.0 O B:HOH303 3.7 34.8 1.0 CE A:LYS35 4.0 34.0 1.0 CG2 A:ILE68 4.0 11.8 1.0 CG1 A:VAL94 4.0 12.6 1.0 CZ2 A:TRP41 4.0 18.6 1.0 ND1 B:HIS90 4.1 21.4 1.0 CD A:LYS35 4.1 31.5 1.0 CH2 A:TRP41 4.2 16.9 1.0 CB B:GLU89 4.4 13.7 1.0 CG B:GLU89 4.5 15.3 1.0 CD1 A:ILE68 4.6 14.3 1.0 NE2 B:HIS90 4.8 25.9 1.0 OE1 B:GLU89 4.9 21.1 1.0

Bromine binding site 6 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-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 Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br201 b:39.6 occ:0.50 CAL B:MKT200 3.8 15.9 0.5 CG2 B:THR106 4.0 16.0 1.0 CG2 B:VAL121 4.1 19.6 1.0 CB B:VAL121 4.2 18.3 1.0 OAP B:MKT200 4.2 17.5 0.5 CB B:THR106 4.3 15.2 1.0 CG1 B:VAL121 4.5 21.9 1.0 CBA B:MKT200 4.6 17.0 0.5 OG1 B:THR106 4.7 19.6 1.0 CAS B:MKT200 4.8 16.5 0.5 OAF B:MKT200 4.8 15.0 0.5

Bromine binding site 7 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br202 b:31.4 occ:0.50 OAH B:MKT200 2.8 17.7 0.5 OG1 B:THR119 3.1 11.7 0.5 OG B:SER117 3.2 11.9 0.5 O B:SER117 3.4 11.6 1.0 CA B:THR118 3.5 12.0 1.0 C B:SER117 3.5 11.8 1.0 N B:THR119 3.6 11.6 1.0 N B:THR118 3.6 10.5 1.0 CAC B:MKT200 3.6 11.1 0.5 C B:THR118 3.6 12.4 1.0 O B:ALA108 3.7 13.3 1.0 CB B:SER117 3.9 13.1 0.5 CB B:THR119 3.9 12.1 0.5 CAU B:MKT200 3.9 16.0 0.5 N B:LEU110 3.9 9.5 1.0 C B:ALA108 4.0 12.2 1.0 CAO B:MKT200 4.0 13.2 0.5 CB B:SER117 4.1 11.5 0.5 CA B:ALA109 4.1 11.1 1.0 CG2 B:THR119 4.1 11.7 0.5 CB B:LEU110 4.2 11.1 1.0 N B:ALA109 4.2 12.0 1.0 CB B:THR119 4.3 11.6 0.5 C B:ALA109 4.3 10.5 1.0 CA B:SER117 4.3 11.3 0.5 CA B:SER117 4.4 10.8 0.5 CB B:ALA108 4.4 12.3 1.0 CA B:THR119 4.4 12.2 0.5 O B:THR118 4.4 15.3 1.0 CAX B:MKT200 4.5 15.4 0.5 CA B:THR119 4.5 11.9 0.5 CA B:LEU110 4.8 9.8 1.0 CAR B:MKT200 4.8 11.8 0.5 CA B:ALA108 4.8 12.1 1.0 CAS B:MKT200 4.9 16.5 0.5 CB B:THR118 4.9 11.2 1.0 OAF B:MKT200 4.9 15.0 0.5 CAK B:MKT200 4.9 12.7 0.5

Bromine binding site 8 out of 8 in the Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of V30M Mutated Transthyretin with Bromide in Complex with Gamma-Mangostin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br203 b:31.1 occ:0.80 O A:HOH310 2.9 39.7 1.0 CE B:LYS35 3.4 35.3 1.0 NZ B:LYS35 3.6 37.1 1.0 CE1 A:HIS90 3.6 26.9 1.0 CG1 B:VAL94 4.0 13.3 1.0 CG2 B:ILE68 4.0 12.8 1.0 CZ2 B:TRP41 4.0 18.0 1.0 CH2 B:TRP41 4.2 15.7 1.0 ND1 A:HIS90 4.2 23.4 1.0 CB A:GLU89 4.3 14.8 1.0 CG A:GLU89 4.3 16.1 1.0 CD1 B:ILE68 4.4 17.1 1.0 NE2 A:HIS90 4.7 30.2 1.0 CD B:LYS35 4.8 33.1 1.0 OE1 A:GLU89 4.9 22.7 1.0

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