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

Other elements in 8zmy:

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

Bromine (Br) 15 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 15 binding sites of Fluorine where determined in the F0502B-Bound Wt Polymorph 5A Alpha-Synuclein Fibril, PDB code: 8zmy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F101

b:60.4
occ:1.00
 F10 C:1KI101 0.0 60.4 1.0
C09 C:1KI101 1.4 60.4 1.0
C08 C:1KI101 2.4 60.4 1.0
OG1 C:THR92 2.9 57.8 1.0
O07 C:1KI101 3.6 60.4 1.0
CB C:ALA90 3.8 54.5 1.0
CB C:THR92 4.3 57.8 1.0
O C:ALA91 4.5 54.9 1.0
C06 C:1KI101 4.5 60.4 1.0
N C:ALA91 4.6 54.9 1.0
C C:ALA91 4.7 54.9 1.0
C C:ALA90 4.8 54.5 1.0
CA C:ALA90 4.8 54.5 1.0
C09 G:1KI103 4.8 60.4 1.0
F10 G:1KI103 4.9 60.4 1.0

Fluorine binding site 2 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F101

b:60.4
occ:1.00
 F10 F:1KI101 0.0 60.4 1.0
C09 F:1KI101 1.4 60.4 1.0
C08 F:1KI101 2.4 60.4 1.0
OG1 F:THR92 2.9 57.8 1.0
O07 F:1KI101 3.6 60.4 1.0
CB F:ALA90 4.0 54.5 1.0
CB F:THR92 4.2 57.8 1.0
O F:ALA91 4.5 54.9 1.0
C06 F:1KI101 4.5 60.4 1.0
N F:ALA91 4.7 54.9 1.0
C F:ALA91 4.7 54.9 1.0
C09 J:1KI102 4.8 60.4 1.0
CG2 F:THR92 4.9 57.8 1.0
C F:ALA90 4.9 54.5 1.0
F10 J:1KI102 4.9 60.4 1.0
CA F:ALA90 5.0 54.5 1.0

Fluorine binding site 3 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F101

b:60.4
occ:1.00
 F10 G:1KI101 0.0 60.4 1.0
C09 G:1KI101 1.4 60.4 1.0
C08 G:1KI101 2.4 60.4 1.0
O H:MET5 2.5 57.0 1.0
C I:MET5 3.2 57.0 1.0
N I:LYS6 3.2 54.5 1.0
CA I:MET5 3.4 57.0 1.0
N I:MET5 3.4 57.0 1.0
CB I:LYS6 3.5 54.5 1.0
O I:PHE4 3.5 53.1 1.0
C I:PHE4 3.6 53.1 1.0
O07 G:1KI101 3.6 60.4 1.0
C H:MET5 3.6 57.0 1.0
O I:MET5 3.7 57.0 1.0
N H:MET5 4.0 57.0 1.0
CA I:LYS6 4.0 54.5 1.0
CE I:LYS6 4.2 54.5 1.0
CB I:PHE4 4.3 53.1 1.0
CA H:MET5 4.4 57.0 1.0
CA I:PHE4 4.5 53.1 1.0
C06 G:1KI101 4.5 60.4 1.0
CG I:LYS6 4.6 54.5 1.0
N H:LYS6 4.6 54.5 1.0
NZ H:LYS6 4.7 54.5 1.0
CA H:LYS6 4.7 54.5 1.0
NZ I:LYS6 4.8 54.5 1.0
CG H:LYS6 4.9 54.5 1.0
CD I:LYS6 4.9 54.5 1.0
CB I:MET5 4.9 57.0 1.0
C H:PHE4 4.9 53.1 1.0
CB H:LYS6 5.0 54.5 1.0

Fluorine binding site 4 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F102

b:60.4
occ:1.00
 F10 G:1KI102 0.0 60.4 1.0
C09 G:1KI102 1.4 60.4 1.0
C08 G:1KI102 2.2 60.4 1.0
OD2 H:ASP2 2.9 62.6 1.0
OD1 H:ASP2 3.1 62.6 1.0
NZ G:LYS10 3.1 52.1 1.0
CE H:LYS10 3.2 52.1 1.0
CG H:ASP2 3.3 62.6 1.0
O07 G:1KI102 3.4 60.4 1.0
NZ H:LYS10 3.4 52.1 1.0
CE G:LYS10 4.0 52.1 1.0
C06 G:1KI102 4.4 60.4 1.0
OD2 G:ASP2 4.5 62.6 1.0
CH3 H:ACE0 4.5 65.8 1.0
CD H:LYS10 4.7 52.1 1.0
N H:MET1 4.7 66.4 1.0
CB H:ASP2 4.8 62.6 1.0
CD G:LYS10 4.8 52.1 1.0
C05 G:1KI102 4.9 60.4 1.0

Fluorine binding site 5 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F103

b:60.4
occ:1.00
 F10 G:1KI103 0.0 60.4 1.0
C09 G:1KI103 1.4 60.4 1.0
C08 G:1KI103 2.4 60.4 1.0
OG1 G:THR92 3.1 57.8 1.0
O07 G:1KI103 3.6 60.4 1.0
CB G:ALA90 3.6 54.5 1.0
N G:ALA91 4.5 54.9 1.0
CB G:THR92 4.5 57.8 1.0
O G:ALA91 4.5 54.9 1.0
C06 G:1KI103 4.5 60.4 1.0
CA G:ALA90 4.6 54.5 1.0
C G:ALA90 4.7 54.5 1.0
C09 H:1KI101 4.7 60.4 1.0
C G:ALA91 4.7 54.9 1.0
F10 H:1KI101 4.9 60.4 1.0
F10 C:1KI101 4.9 60.4 1.0

Fluorine binding site 6 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F104

b:60.4
occ:1.00
 F10 G:1KI104 0.0 60.4 1.0
C09 G:1KI104 1.4 60.4 1.0
O H:LYS10 2.3 52.1 1.0
C08 G:1KI104 2.3 60.4 1.0
O07 G:1KI104 2.5 60.4 1.0
C H:LYS10 3.0 52.1 1.0
N H:ALA11 3.5 53.6 1.0
CA H:ALA11 3.6 53.6 1.0
C06 G:1KI104 3.8 60.4 1.0
CA H:LYS10 4.0 52.1 1.0
C H:ALA11 4.1 53.6 1.0
O I:ALA11 4.2 53.6 1.0
CB H:LYS10 4.3 52.1 1.0
O H:ALA11 4.3 53.6 1.0
CA I:LYS10 4.4 52.1 1.0
N I:ALA11 4.6 53.6 1.0
C I:LYS10 4.6 52.1 1.0
N H:LYS12 4.8 55.7 1.0
C05 G:1KI104 4.9 60.4 1.0
CB H:ALA11 4.9 53.6 1.0
CG H:LYS12 5.0 55.7 1.0

Fluorine binding site 7 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F101

b:60.4
occ:1.00
 F10 H:1KI101 0.0 60.4 1.0
C09 H:1KI101 1.4 60.4 1.0
C08 H:1KI101 2.4 60.4 1.0
OG1 H:THR92 3.2 57.8 1.0
CB H:ALA90 3.5 54.5 1.0
O07 H:1KI101 3.6 60.4 1.0
N H:ALA91 4.4 54.9 1.0
CA H:ALA90 4.5 54.5 1.0
O H:ALA91 4.5 54.9 1.0
C06 H:1KI101 4.5 60.4 1.0
CB H:THR92 4.6 57.8 1.0
C H:ALA90 4.6 54.5 1.0
C H:ALA91 4.7 54.9 1.0
F10 G:1KI103 4.9 60.4 1.0

Fluorine binding site 8 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F102

b:60.4
occ:1.00
 F10 H:1KI102 0.0 60.4 1.0
C09 H:1KI102 1.4 60.4 1.0
O I:GLY41 2.3 52.8 1.0
C08 H:1KI102 2.3 60.4 1.0
O07 H:1KI102 2.5 60.4 1.0
C I:GLY41 2.8 52.8 1.0
CA I:GLY41 2.9 52.8 1.0
O07 J:1KI101 3.7 60.4 1.0
C06 H:1KI102 3.9 60.4 1.0
N I:SER42 3.9 53.7 1.0
N I:GLY41 4.3 52.8 1.0
C06 J:1KI101 4.4 60.4 1.0
O I:SER42 4.6 53.7 1.0
C05 H:1KI102 4.6 60.4 1.0
CA I:SER42 4.6 53.7 1.0
C I:SER42 4.8 53.7 1.0
C09 J:1KI101 4.8 60.4 1.0
C08 J:1KI101 4.8 60.4 1.0
CD K:LYS10 5.0 52.1 1.0

Fluorine binding site 9 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F103

b:60.4
occ:1.00
 F10 H:1KI103 0.0 60.4 1.0
C09 H:1KI103 1.4 60.4 1.0
C I:ACE0 2.3 65.8 1.0
C08 H:1KI103 2.4 60.4 1.0
O H:ACE0 2.4 65.8 1.0
CH3 I:ACE0 2.5 65.8 1.0
O I:ACE0 2.6 65.8 1.0
N I:MET1 2.9 66.4 1.0
O07 H:1KI103 3.3 60.4 1.0
C H:ACE0 3.5 65.8 1.0
CB I:MET1 3.5 66.4 1.0
CA I:MET1 3.8 66.4 1.0
CE L:MET1 4.0 66.4 1.0
CH3 H:ACE0 4.2 65.8 1.0
N H:MET1 4.4 66.4 1.0
CG1 L:VAL40 4.5 52.1 1.0
C06 H:1KI103 4.5 60.4 1.0
CE I:MET1 4.6 66.4 1.0
CA H:MET1 4.7 66.4 1.0
C05 H:1KI103 4.8 60.4 1.0
CG I:MET1 4.9 66.4 1.0
CB H:MET1 4.9 66.4 1.0
C I:MET1 5.0 66.4 1.0

Fluorine binding site 10 out of 15 in 8zmy

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Fluorine 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 Fluorine with other atoms in the F 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:F101

b:60.4
occ:1.00
 F10 J:1KI101 0.0 60.4 1.0
C09 J:1KI101 1.4 60.4 1.0
C08 J:1KI101 2.2 60.4 1.0
OD2 K:ASP2 2.9 62.6 1.0
NZ J:LYS10 3.0 52.1 1.0
OD1 K:ASP2 3.1 62.6 1.0
CE K:LYS10 3.2 52.1 1.0
CG K:ASP2 3.3 62.6 1.0
O07 J:1KI101 3.4 60.4 1.0
NZ K:LYS10 3.5 52.1 1.0
CE J:LYS10 3.9 52.1 1.0
C06 J:1KI101 4.4 60.4 1.0
OD2 J:ASP2 4.4 62.6 1.0
CH3 K:ACE0 4.6 65.8 1.0
CD K:LYS10 4.6 52.1 1.0
CD J:LYS10 4.7 52.1 1.0
N K:MET1 4.7 66.4 1.0
CB K:ASP2 4.8 62.6 1.0
C05 J:1KI101 4.9 60.4 1.0

Reference:

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
Page generated: Sat Sep 28 20:42:03 2024

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