Bromine in PDB 8zmy: F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril

The structure of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril also contains other interesting chemical elements:

Fluorine

(F)

15 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Bromine atom in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril (pdb code 8zmy). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 15 binding sites of Bromine where determined in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril, PDB code: 8zmy:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ C:Br101 b:60.4 occ:1.00 BR2 C:1KI101 0.0 60.4 1.0 C21 C:1KI101 1.9 60.4 1.0 C20 C:1KI101 2.9 60.4 1.0 C23 C:1KI101 2.9 60.4 1.0 O24 C:1KI101 3.1 60.4 1.0 O B:GLY84 3.6 59.1 1.0 C B:GLY84 3.8 59.1 1.0 N A:GLY86 3.8 57.5 1.0 N A:ALA85 3.8 57.0 1.0 CA A:GLY86 3.9 57.5 1.0 CA A:GLY84 4.0 59.1 1.0 C A:ALA85 4.1 57.0 1.0 CA B:GLY84 4.2 59.1 1.0 C19 C:1KI101 4.2 60.4 1.0 C25 C:1KI101 4.2 60.4 1.0 N B:ALA85 4.2 57.0 1.0 C A:GLY84 4.3 59.1 1.0 N B:GLY86 4.4 57.5 1.0 CA B:ALA85 4.4 57.0 1.0 O A:ALA85 4.5 57.0 1.0 CA A:ALA85 4.6 57.0 1.0 O B:GLY86 4.6 57.5 1.0 C26 C:1KI101 4.7 60.4 1.0 C A:GLY86 4.9 57.5 1.0 C B:ALA85 4.9 57.0 1.0 BR2 G:1KI103 4.9 60.4 1.0

Bromine binding site 2 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ F:Br101 b:60.4 occ:1.00 BR2 F:1KI101 0.0 60.4 1.0 C21 F:1KI101 1.9 60.4 1.0 C20 F:1KI101 2.9 60.4 1.0 C23 F:1KI101 2.9 60.4 1.0 O24 F:1KI101 3.1 60.4 1.0 O E:GLY84 3.7 59.1 1.0 C E:GLY84 3.8 59.1 1.0 N D:GLY86 4.0 57.5 1.0 N D:ALA85 4.1 57.0 1.0 CA D:GLY86 4.1 57.5 1.0 CA E:GLY84 4.1 59.1 1.0 C19 F:1KI101 4.2 60.4 1.0 C25 F:1KI101 4.2 60.4 1.0 CA D:GLY84 4.2 59.1 1.0 N E:ALA85 4.3 57.0 1.0 C D:ALA85 4.4 57.0 1.0 N E:GLY86 4.4 57.5 1.0 CA E:ALA85 4.5 57.0 1.0 C D:GLY84 4.6 59.1 1.0 O E:GLY86 4.6 57.5 1.0 C26 F:1KI101 4.7 60.4 1.0 O D:ALA85 4.8 57.0 1.0 CA D:ALA85 4.9 57.0 1.0 BR2 J:1KI102 5.0 60.4 1.0 C E:ALA85 5.0 57.0 1.0

Bromine binding site 3 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ G:Br101 b:60.4 occ:1.00 BR2 G:1KI101 0.0 60.4 1.0 C21 G:1KI101 1.9 60.4 1.0 O B:MET5 2.7 57.0 1.0 C20 G:1KI101 2.9 60.4 1.0 C23 G:1KI101 2.9 60.4 1.0 C B:MET5 3.0 57.0 1.0 O24 G:1KI101 3.1 60.4 1.0 NZ B:LYS6 3.4 54.5 1.0 N B:MET5 3.5 57.0 1.0 CB B:LYS6 3.5 54.5 1.0 N B:LYS6 3.5 54.5 1.0 CE B:LYS6 3.6 54.5 1.0 CA B:MET5 3.8 57.0 1.0 CG B:LYS6 3.8 54.5 1.0 CA B:LYS6 3.9 54.5 1.0 C B:PHE4 4.1 53.1 1.0 C19 G:1KI101 4.2 60.4 1.0 C25 G:1KI101 4.2 60.4 1.0 CD B:LYS6 4.3 54.5 1.0 O A:MET5 4.5 57.0 1.0 CB B:PHE4 4.5 53.1 1.0 CA B:PHE4 4.6 53.1 1.0 O B:PHE4 4.7 53.1 1.0 C26 G:1KI101 4.7 60.4 1.0 O C:PHE4 4.9 53.1 1.0

Bromine binding site 4 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ G:Br102 b:60.4 occ:1.00 BR2 G:1KI102 0.0 60.4 1.0 C21 G:1KI102 1.9 60.4 1.0 O A:LYS10 2.7 52.1 1.0 C20 G:1KI102 2.9 60.4 1.0 C23 G:1KI102 2.9 60.4 1.0 BR2 G:1KI104 3.0 60.4 1.0 C21 G:1KI104 3.1 60.4 1.0 O24 G:1KI102 3.1 60.4 1.0 C20 G:1KI104 3.6 60.4 1.0 C23 G:1KI104 3.6 60.4 1.0 CA B:LYS10 3.7 52.1 1.0 C A:LYS10 3.8 52.1 1.0 O24 G:1KI104 3.9 60.4 1.0 C B:LYS10 4.1 52.1 1.0 CB B:LYS10 4.1 52.1 1.0 C19 G:1KI102 4.2 60.4 1.0 C25 G:1KI102 4.2 60.4 1.0 CB A:LYS10 4.2 52.1 1.0 C19 G:1KI104 4.4 60.4 1.0 C25 G:1KI104 4.5 60.4 1.0 CA A:LYS10 4.5 52.1 1.0 O B:LYS10 4.5 52.1 1.0 N B:ALA11 4.6 53.6 1.0 N A:ALA11 4.7 53.6 1.0 C26 G:1KI102 4.7 60.4 1.0 N B:LYS10 4.8 52.1 1.0 C26 G:1KI104 4.8 60.4 1.0 CA A:ALA11 4.8 53.6 1.0 CG B:LYS10 4.8 52.1 1.0 O B:ALA11 5.0 53.6 1.0

Bromine binding site 5 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ G:Br103 b:60.4 occ:1.00 BR2 G:1KI103 0.0 60.4 1.0 C21 G:1KI103 1.9 60.4 1.0 C20 G:1KI103 2.9 60.4 1.0 C23 G:1KI103 2.9 60.4 1.0 O24 G:1KI103 3.1 60.4 1.0 O C:GLY84 3.5 59.1 1.0 C C:GLY84 3.6 59.1 1.0 N B:ALA85 3.9 57.0 1.0 C20 C:1KI101 4.0 60.4 1.0 CA B:GLY84 4.0 59.1 1.0 CA C:GLY84 4.0 59.1 1.0 N B:GLY86 4.0 57.5 1.0 CA B:GLY86 4.1 57.5 1.0 N C:ALA85 4.2 57.0 1.0 C19 G:1KI103 4.2 60.4 1.0 C25 G:1KI103 4.2 60.4 1.0 C19 C:1KI101 4.2 60.4 1.0 C B:ALA85 4.3 57.0 1.0 C21 C:1KI101 4.3 60.4 1.0 C B:GLY84 4.4 59.1 1.0 N C:GLY86 4.4 57.5 1.0 CA C:ALA85 4.4 57.0 1.0 C18 C:1KI101 4.6 60.4 1.0 O B:ALA85 4.7 57.0 1.0 C26 G:1KI103 4.7 60.4 1.0 CA B:ALA85 4.7 57.0 1.0 O C:GLY86 4.8 57.5 1.0 C17 C:1KI101 4.8 60.4 1.0 BR2 H:1KI101 4.8 60.4 1.0 C26 C:1KI101 4.8 60.4 1.0 C23 C:1KI101 4.9 60.4 1.0 BR2 C:1KI101 4.9 60.4 1.0 C C:ALA85 5.0 57.0 1.0 N B:GLY84 5.0 59.1 1.0

Bromine binding site 6 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ G:Br104 b:60.4 occ:1.00 BR2 G:1KI104 0.0 60.4 1.0 C21 G:1KI104 1.9 60.4 1.0 CA A:ALA11 2.3 53.6 1.0 O A:LYS10 2.4 52.1 1.0 O B:ALA11 2.6 53.6 1.0 C A:ALA11 2.8 53.6 1.0 C20 G:1KI104 2.9 60.4 1.0 C23 G:1KI104 2.9 60.4 1.0 N A:ALA11 3.0 53.6 1.0 C A:LYS10 3.0 52.1 1.0 BR2 G:1KI102 3.0 60.4 1.0 O24 G:1KI104 3.1 60.4 1.0 N A:LYS12 3.3 55.7 1.0 CB A:ALA11 3.5 53.6 1.0 O A:ALA11 3.5 53.6 1.0 N B:ALA11 3.5 53.6 1.0 C B:ALA11 3.7 53.6 1.0 C B:LYS10 4.0 52.1 1.0 C19 G:1KI104 4.2 60.4 1.0 C25 G:1KI104 4.2 60.4 1.0 CA B:LYS10 4.2 52.1 1.0 CA B:ALA11 4.2 53.6 1.0 CG A:LYS12 4.4 55.7 1.0 CA A:LYS10 4.4 52.1 1.0 CA A:LYS12 4.4 55.7 1.0 CB A:LYS12 4.4 55.7 1.0 CG B:LYS12 4.5 55.7 1.0 C26 G:1KI104 4.7 60.4 1.0 N B:LYS10 4.8 52.1 1.0 N B:LYS12 4.8 55.7 1.0 C21 G:1KI102 4.8 60.4 1.0 O B:LYS10 4.9 52.1 1.0 CD A:LYS12 4.9 55.7 1.0

Bromine binding site 7 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ H:Br101 b:60.4 occ:1.00 BR2 H:1KI101 0.0 60.4 1.0 C21 H:1KI101 1.9 60.4 1.0 C20 H:1KI101 2.9 60.4 1.0 C23 H:1KI101 2.9 60.4 1.0 O24 H:1KI101 3.1 60.4 1.0 O G:GLY84 3.4 59.1 1.0 C G:GLY84 3.5 59.1 1.0 CA G:GLY84 3.8 59.1 1.0 C20 G:1KI103 3.8 60.4 1.0 CA C:GLY84 3.9 59.1 1.0 N C:ALA85 3.9 57.0 1.0 N G:ALA85 4.1 57.0 1.0 C19 G:1KI103 4.1 60.4 1.0 N C:GLY86 4.2 57.5 1.0 C19 H:1KI101 4.2 60.4 1.0 C25 H:1KI101 4.2 60.4 1.0 C21 G:1KI103 4.2 60.4 1.0 C C:GLY84 4.3 59.1 1.0 CA C:GLY86 4.4 57.5 1.0 C C:ALA85 4.4 57.0 1.0 CA G:ALA85 4.4 57.0 1.0 C18 G:1KI103 4.5 60.4 1.0 N G:GLY86 4.6 57.5 1.0 C26 H:1KI101 4.7 60.4 1.0 C26 G:1KI103 4.7 60.4 1.0 C17 G:1KI103 4.8 60.4 1.0 C23 G:1KI103 4.8 60.4 1.0 CA C:ALA85 4.8 57.0 1.0 BR2 G:1KI103 4.8 60.4 1.0 O C:ALA85 4.8 57.0 1.0 N C:GLY84 4.9 59.1 1.0

Bromine binding site 8 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ H:Br102 b:60.4 occ:1.00 BR2 H:1KI102 0.0 60.4 1.0 C21 H:1KI102 1.9 60.4 1.0 O C:GLY41 2.6 52.8 1.0 C20 H:1KI102 2.9 60.4 1.0 C23 H:1KI102 2.9 60.4 1.0 O24 H:1KI102 3.1 60.4 1.0 O B:SER42 3.3 53.7 1.0 CA C:SER42 3.5 53.7 1.0 N C:LYS43 3.7 53.4 1.0 C C:GLY41 3.7 52.8 1.0 C C:SER42 3.7 53.7 1.0 O B:GLY41 3.8 52.8 1.0 C B:GLY41 3.8 52.8 1.0 C B:SER42 4.0 53.7 1.0 N C:SER42 4.1 53.7 1.0 C19 H:1KI102 4.2 60.4 1.0 C25 H:1KI102 4.2 60.4 1.0 CA B:GLY41 4.2 52.8 1.0 N B:SER42 4.2 53.7 1.0 CB C:LYS43 4.2 53.4 1.0 C25 J:1KI101 4.2 60.4 1.0 O C:SER42 4.5 53.7 1.0 CA C:LYS43 4.6 53.4 1.0 CA B:SER42 4.7 53.7 1.0 C26 H:1KI102 4.7 60.4 1.0 CB C:SER42 4.7 53.7 1.0 CB B:LYS43 4.8 53.4 1.0 C26 J:1KI101 4.8 60.4 1.0 N B:LYS43 4.8 53.4 1.0 CA B:LYS43 5.0 53.4 1.0

Bromine binding site 9 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ H:Br103 b:60.4 occ:1.00 BR2 H:1KI103 0.0 60.4 1.0 C21 H:1KI103 1.9 60.4 1.0 O B:ACE0 2.4 65.8 1.0 CE E:MET1 2.4 66.4 1.0 C20 H:1KI103 2.9 60.4 1.0 C23 H:1KI103 2.9 60.4 1.0 C B:ACE0 3.0 65.8 1.0 O24 H:1KI103 3.1 60.4 1.0 CH3 B:ACE0 3.1 65.8 1.0 N B:MET1 4.1 66.4 1.0 SD E:MET1 4.1 66.4 1.0 C19 H:1KI103 4.2 60.4 1.0 C25 H:1KI103 4.2 60.4 1.0 O A:ACE0 4.4 65.8 1.0 CB B:MET1 4.5 66.4 1.0 CG1 F:VAL40 4.5 52.1 1.0 C26 H:1KI103 4.7 60.4 1.0 CE B:MET1 4.7 66.4 1.0 CA B:MET1 4.8 66.4 1.0 CG1 E:VAL40 4.8 52.1 1.0 CE F:MET1 5.0 66.4 1.0

Bromine binding site 10 out of 15 in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril within 5.0Å range: probe atom residue distance (Å) B Occ J:Br101 b:60.4 occ:1.00 BR2 J:1KI101 0.0 60.4 1.0 C21 J:1KI101 1.9 60.4 1.0 O D:LYS10 2.8 52.1 1.0 C20 J:1KI101 2.9 60.4 1.0 C23 J:1KI101 2.9 60.4 1.0 BR2 J:1KI103 3.0 60.4 1.0 C21 J:1KI103 3.1 60.4 1.0 O24 J:1KI101 3.1 60.4 1.0 C20 J:1KI103 3.5 60.4 1.0 C23 J:1KI103 3.6 60.4 1.0 CA E:LYS10 3.8 52.1 1.0 C D:LYS10 3.8 52.1 1.0 O24 J:1KI103 3.9 60.4 1.0 C E:LYS10 4.2 52.1 1.0 C19 J:1KI101 4.2 60.4 1.0 C25 J:1KI101 4.2 60.4 1.0 CB E:LYS10 4.3 52.1 1.0 CB D:LYS10 4.3 52.1 1.0 C19 J:1KI103 4.4 60.4 1.0 C25 J:1KI103 4.4 60.4 1.0 N E:ALA11 4.6 53.6 1.0 O E:LYS10 4.6 52.1 1.0 CA D:LYS10 4.6 52.1 1.0 N D:ALA11 4.7 53.6 1.0 C26 J:1KI101 4.7 60.4 1.0 CA D:ALA11 4.8 53.6 1.0 C26 J:1KI103 4.8 60.4 1.0 O E:ALA11 4.9 53.6 1.0 N E:LYS10 4.9 52.1 1.0 CG E:LYS10 5.0 52.1 1.0

K.Liu, Y.Tao, Q.Zhao, W.Xia, X.Li, S.Zhang, Y.Yao, H.Xiang, C.Han, L.Tan, B.Sun, D.Li, A.Li, C.Liu. Binding Adaptability of Chemical Ligands to Polymorphic Alpha-Synuclein Amyloid Fibrils. Proc.Natl.Acad.Sci.Usa V. 121 33121 2024.
ISSN: ESSN 1091-6490
PubMed: 39172784
DOI: 10.1073/PNAS.2321633121