Chlorine in PDB 9fyp: Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. (pdb code 9fyp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH., PDB code: 9fyp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 9fyp

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Chlorine binding site 1 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl201

b:39.8
occ:1.00
 O I:HOH303 3.3 31.9 1.0
O I:VAL52 3.4 34.9 1.0
N I:GLY51 3.5 29.6 1.0
O K:GLY51 3.6 31.7 1.0
C I:VAL52 3.6 22.5 1.0
N I:VAL52 3.8 26.6 1.0
N I:ALA53 3.9 22.3 1.0
O K:HIS50 3.9 26.7 1.0
CB I:ALA53 4.0 26.4 1.0
C I:HIS50 4.1 26.6 1.0
C I:GLY51 4.1 26.0 1.0
N K:ALA53 4.1 21.3 1.0
CB I:HIS50 4.1 24.9 1.0
CA I:ALA53 4.2 24.4 1.0
CB K:ALA53 4.2 24.9 1.0
CA I:GLY51 4.2 26.5 1.0
CA I:HIS50 4.3 21.1 1.0
C K:GLY51 4.3 23.5 1.0
CA I:VAL52 4.3 27.1 1.0
C K:HIS50 4.4 26.6 1.0
CB K:HIS50 4.4 21.5 1.0
CL K:CL201 4.7 42.3 1.0
ND1 I:HIS50 4.7 33.8 1.0
O I:GLY51 4.7 31.9 1.0
CA K:VAL52 4.8 24.6 1.0
C K:VAL52 4.8 20.2 1.0
CA K:ALA53 4.8 22.0 1.0
N K:VAL52 4.8 23.9 1.0
O I:HIS50 4.9 30.1 1.0
N K:GLY51 4.9 27.9 1.0
CG I:HIS50 4.9 31.5 1.0

Chlorine binding site 2 out of 10 in 9fyp

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Chlorine binding site 2 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl201

b:45.5
occ:1.00
 O J:HOH302 3.2 32.0 1.0
O J:VAL52 3.4 35.0 1.0
N J:GLY51 3.5 30.7 1.0
C J:VAL52 3.6 20.8 1.0
O L:GLY51 3.6 32.5 1.0
N J:VAL52 3.8 27.2 1.0
N J:ALA53 3.8 23.4 1.0
O L:HIS50 3.9 30.2 1.0
CB J:ALA53 4.0 29.3 1.0
C J:HIS50 4.0 26.9 1.0
C J:GLY51 4.0 25.7 1.0
CB J:HIS50 4.1 24.1 1.0
CA J:ALA53 4.1 24.8 1.0
N L:ALA53 4.2 22.4 1.0
CA J:GLY51 4.2 28.8 1.0
CA J:HIS50 4.2 21.6 1.0
CB L:ALA53 4.3 27.2 1.0
CA J:VAL52 4.3 26.4 1.0
C L:GLY51 4.4 28.0 1.0
CB L:HIS50 4.4 25.8 1.0
C L:HIS50 4.4 30.2 1.0
O J:GLY51 4.7 34.0 1.0
ND1 J:HIS50 4.7 35.9 1.0
O J:HIS50 4.8 29.9 1.0
CA L:VAL52 4.9 27.1 1.0
C L:VAL52 4.9 21.4 1.0
CA L:ALA53 4.9 25.0 1.0
CG J:HIS50 4.9 31.9 1.0
CL L:CL201 4.9 41.3 1.0
N L:VAL52 4.9 25.1 1.0
N L:GLY51 5.0 30.2 1.0

Chlorine binding site 3 out of 10 in 9fyp

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Chlorine binding site 3 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl201

b:42.3
occ:1.00
 O K:HOH302 3.2 30.3 1.0
N K:GLY51 3.5 27.9 1.0
O K:VAL52 3.5 31.0 1.0
O M:GLY51 3.5 32.1 1.0
C K:VAL52 3.7 20.2 1.0
N K:VAL52 3.8 23.9 1.0
O M:HIS50 3.9 30.1 1.0
N K:ALA53 3.9 21.3 1.0
C K:HIS50 4.0 26.6 1.0
CB K:HIS50 4.0 21.5 1.0
CB K:ALA53 4.0 24.9 1.0
C K:GLY51 4.1 23.5 1.0
CA K:HIS50 4.2 18.7 1.0
N M:ALA53 4.2 21.5 1.0
CA K:GLY51 4.2 25.3 1.0
CA K:ALA53 4.2 22.0 1.0
CB M:ALA53 4.3 26.8 1.0
C M:GLY51 4.3 28.0 1.0
CB M:HIS50 4.4 25.2 1.0
C M:HIS50 4.4 27.9 1.0
CA K:VAL52 4.4 24.6 1.0
ND1 K:HIS50 4.6 34.5 1.0
CL I:CL201 4.7 39.8 1.0
O K:GLY51 4.7 31.7 1.0
O K:HIS50 4.8 26.7 1.0
CG K:HIS50 4.8 30.8 1.0
CA M:VAL52 4.9 26.1 1.0
C M:VAL52 4.9 18.0 1.0
CL M:CL201 4.9 44.2 1.0
N M:VAL52 4.9 26.1 1.0
N M:GLY51 4.9 29.2 1.0
CA M:ALA53 4.9 26.4 1.0

Chlorine binding site 4 out of 10 in 9fyp

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Chlorine binding site 4 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl201

b:41.3
occ:1.00
 O L:HOH302 3.2 31.7 1.0
O L:VAL52 3.5 34.2 1.0
N L:GLY51 3.5 30.2 1.0
O N:GLY51 3.5 32.1 1.0
C L:VAL52 3.7 21.4 1.0
O N:HIS50 3.8 28.9 1.0
N L:VAL52 3.9 25.1 1.0
N L:ALA53 4.0 22.4 1.0
C L:HIS50 4.0 30.2 1.0
CB L:HIS50 4.1 25.8 1.0
CB L:ALA53 4.1 27.2 1.0
N N:ALA53 4.1 19.1 1.0
C L:GLY51 4.1 28.0 1.0
CA L:HIS50 4.2 23.4 1.0
CB N:ALA53 4.2 25.4 1.0
C N:GLY51 4.2 23.9 1.0
CA L:GLY51 4.2 28.1 1.0
CA L:ALA53 4.3 25.0 1.0
CB N:HIS50 4.3 21.1 1.0
C N:HIS50 4.3 24.8 1.0
CA L:VAL52 4.4 27.1 1.0
ND1 L:HIS50 4.7 37.0 1.0
CL N:CL201 4.7 41.0 1.0
C N:VAL52 4.8 17.3 1.0
CA N:VAL52 4.8 22.8 1.0
O L:GLY51 4.8 32.5 1.0
N N:GLY51 4.8 26.2 1.0
N N:VAL52 4.8 25.1 1.0
CA N:ALA53 4.8 21.3 1.0
O L:HIS50 4.9 30.2 1.0
CG L:HIS50 4.9 34.4 1.0
CL J:CL201 4.9 45.5 1.0
CA N:HIS50 5.0 17.8 1.0

Chlorine binding site 5 out of 10 in 9fyp

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Chlorine binding site 5 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl201

b:44.2
occ:1.00
 O M:HOH302 3.3 29.9 1.0
O M:VAL52 3.5 35.1 1.0
N M:GLY51 3.5 29.2 1.0
O O:GLY51 3.5 33.0 1.0
C M:VAL52 3.7 18.0 1.0
O O:HIS50 3.8 31.6 1.0
N M:VAL52 3.8 26.1 1.0
N M:ALA53 4.0 21.5 1.0
C M:HIS50 4.0 27.9 1.0
C M:GLY51 4.1 28.0 1.0
CB M:HIS50 4.1 25.2 1.0
N O:ALA53 4.1 21.4 1.0
CB M:ALA53 4.2 26.8 1.0
CA M:GLY51 4.2 27.1 1.0
C O:GLY51 4.2 28.6 1.0
CA M:HIS50 4.2 22.0 1.0
CB O:ALA53 4.3 28.2 1.0
C O:HIS50 4.3 29.5 1.0
CA M:ALA53 4.3 26.4 1.0
CB O:HIS50 4.3 27.1 1.0
CA M:VAL52 4.4 26.1 1.0
ND1 M:HIS50 4.7 36.8 1.0
CA O:VAL52 4.7 25.6 1.0
O M:GLY51 4.7 32.1 1.0
C O:VAL52 4.7 20.0 1.0
N O:GLY51 4.8 29.5 1.0
N O:VAL52 4.8 28.1 1.0
CL O:CL201 4.8 43.0 1.0
CA O:ALA53 4.8 25.0 1.0
O M:HIS50 4.8 30.1 1.0
CL K:CL201 4.9 42.3 1.0
CG M:HIS50 4.9 33.7 1.0
CA O:HIS50 5.0 23.2 1.0

Chlorine binding site 6 out of 10 in 9fyp

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Chlorine binding site 6 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl201

b:41.0
occ:1.00
 O N:HOH302 3.2 26.9 1.0
O N:VAL52 3.4 31.6 1.0
N N:GLY51 3.4 26.2 1.0
O P:GLY51 3.5 34.1 1.0
C N:VAL52 3.7 17.3 1.0
N N:VAL52 3.8 25.1 1.0
O P:HIS50 3.8 31.1 1.0
N N:ALA53 4.0 19.1 1.0
C N:HIS50 4.0 24.8 1.0
C N:GLY51 4.1 23.9 1.0
CB N:HIS50 4.1 21.1 1.0
CB N:ALA53 4.1 25.4 1.0
N P:ALA53 4.2 21.6 1.0
CA N:GLY51 4.2 24.8 1.0
CA N:HIS50 4.2 17.8 1.0
C P:GLY51 4.2 27.8 1.0
CA N:ALA53 4.3 21.3 1.0
CB P:ALA53 4.3 27.8 1.0
C P:HIS50 4.3 28.8 1.0
CB P:HIS50 4.3 24.1 1.0
CA N:VAL52 4.4 22.8 1.0
ND1 N:HIS50 4.7 35.0 1.0
CL L:CL201 4.7 41.3 1.0
O N:GLY51 4.7 32.1 1.0
CA P:VAL52 4.8 26.1 1.0
C P:VAL52 4.8 20.0 1.0
CL P:CL201 4.8 43.1 1.0
N P:VAL52 4.8 27.6 1.0
N P:GLY51 4.8 29.0 1.0
O N:HIS50 4.8 28.9 1.0
CA P:ALA53 4.9 24.9 1.0
CG N:HIS50 4.9 31.9 1.0

Chlorine binding site 7 out of 10 in 9fyp

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Chlorine binding site 7 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cl201

b:43.0
occ:1.00
 O O:HOH302 3.3 32.0 1.0
O O:VAL52 3.4 36.0 1.0
O Q:GLY51 3.5 34.1 1.0
N O:GLY51 3.5 29.5 1.0
C O:VAL52 3.7 20.0 1.0
O Q:HIS50 3.8 32.4 1.0
N O:VAL52 3.9 28.1 1.0
N O:ALA53 4.0 21.4 1.0
C O:HIS50 4.1 29.5 1.0
N Q:ALA53 4.1 21.3 1.0
CB O:HIS50 4.1 27.1 1.0
CB O:ALA53 4.2 28.2 1.0
C O:GLY51 4.2 28.6 1.0
C Q:GLY51 4.2 26.5 1.0
CB Q:ALA53 4.2 27.3 1.0
CA O:HIS50 4.3 23.2 1.0
CA O:GLY51 4.3 27.9 1.0
C Q:HIS50 4.3 28.8 1.0
CB Q:HIS50 4.3 22.7 1.0
CA O:ALA53 4.3 25.0 1.0
CA O:VAL52 4.4 25.6 1.0
ND1 O:HIS50 4.7 37.1 1.0
CL Q:CL201 4.7 40.6 1.0
C Q:VAL52 4.7 18.1 1.0
CA Q:VAL52 4.7 24.3 1.0
N Q:VAL52 4.7 26.0 1.0
N Q:GLY51 4.8 27.9 1.0
CA Q:ALA53 4.8 23.1 1.0
CL M:CL201 4.8 44.2 1.0
O O:GLY51 4.9 33.0 1.0
CG O:HIS50 4.9 35.2 1.0
O O:HIS50 4.9 31.6 1.0
CA Q:HIS50 5.0 20.6 1.0

Chlorine binding site 8 out of 10 in 9fyp

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Chlorine binding site 8 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl201

b:43.1
occ:1.00
 O P:HOH302 3.3 31.8 1.0
O P:VAL52 3.4 35.9 1.0
N P:GLY51 3.5 29.0 1.0
O R:GLY51 3.5 33.6 1.0
C P:VAL52 3.7 20.0 1.0
O R:HIS50 3.8 34.8 1.0
N P:VAL52 3.8 27.6 1.0
N P:ALA53 4.0 21.6 1.0
C P:HIS50 4.1 28.8 1.0
CB P:ALA53 4.1 27.8 1.0
C P:GLY51 4.1 27.8 1.0
CB P:HIS50 4.1 24.1 1.0
N R:ALA53 4.1 22.4 1.0
CA P:GLY51 4.2 29.3 1.0
C R:GLY51 4.2 29.5 1.0
CA P:HIS50 4.3 23.3 1.0
CA P:ALA53 4.3 24.9 1.0
CB R:ALA53 4.3 28.0 1.0
C R:HIS50 4.3 30.3 1.0
CB R:HIS50 4.4 24.9 1.0
CA P:VAL52 4.4 26.1 1.0
ND1 P:HIS50 4.7 36.0 1.0
CA R:VAL52 4.8 26.3 1.0
C R:VAL52 4.8 20.1 1.0
O P:GLY51 4.8 34.1 1.0
CL N:CL201 4.8 41.0 1.0
N R:VAL52 4.8 28.8 1.0
N R:GLY51 4.8 30.9 1.0
CA R:ALA53 4.8 25.1 1.0
CL R:CL201 4.9 41.5 1.0
O P:HIS50 4.9 31.1 1.0
CG P:HIS50 4.9 34.3 1.0

Chlorine binding site 9 out of 10 in 9fyp

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Chlorine binding site 9 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cl201

b:40.6
occ:1.00
 O Q:HOH303 3.2 31.7 1.0
O Q:VAL52 3.4 33.3 1.0
N Q:GLY51 3.6 27.9 1.0
C Q:VAL52 3.7 18.1 1.0
N Q:VAL52 3.8 26.0 1.0
N Q:ALA53 4.0 21.3 1.0
C Q:HIS50 4.1 28.8 1.0
C Q:GLY51 4.1 26.5 1.0
CB Q:ALA53 4.1 27.3 1.0
CB Q:HIS50 4.2 22.7 1.0
CA Q:GLY51 4.3 28.2 1.0
CA Q:ALA53 4.3 23.1 1.0
CA Q:HIS50 4.3 20.6 1.0
CA Q:VAL52 4.4 24.3 1.0
CL O:CL201 4.7 43.0 1.0
ND1 Q:HIS50 4.7 35.2 1.0
O Q:GLY51 4.8 34.1 1.0
O Q:HIS50 4.9 32.4 1.0
CG Q:HIS50 5.0 33.4 1.0

Chlorine binding site 10 out of 10 in 9fyp

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Chlorine binding site 10 out of 10 in the Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Cryo Em Structure of the Type 3B Polymorph of Alpha-Synuclein at Low pH. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl201

b:41.5
occ:1.00
 O R:HOH303 3.2 35.4 1.0
O R:VAL52 3.4 36.2 1.0
N R:GLY51 3.7 30.9 1.0
C R:VAL52 3.7 20.1 1.0
N R:VAL52 3.9 28.8 1.0
N R:ALA53 4.0 22.4 1.0
CB R:ALA53 4.2 28.0 1.0
C R:HIS50 4.2 30.3 1.0
CB R:HIS50 4.2 24.9 1.0
C R:GLY51 4.2 29.5 1.0
CA R:ALA53 4.3 25.1 1.0
CA R:GLY51 4.4 29.9 1.0
CA R:HIS50 4.4 24.2 1.0
CA R:VAL52 4.5 26.3 1.0
ND1 R:HIS50 4.7 37.8 1.0
CL P:CL201 4.9 43.1 1.0
O R:GLY51 4.9 33.6 1.0

Reference:

L.Frey, D.Ghosh, B.M.Qureshi, D.Rhyner, R.Guerrero-Ferreira, A.Pokharna, W.Kwiatkowski, T.Serdiuk, P.Picotti, R.Riek, J.Greenwald. On the pH-Dependence of Alpha-Synuclein Amyloid Polymorphism and the Role of Secondary Nucleation in Seed-Based Amyloid Propagation Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.1101/2023.06.25.546428
Page generated: Tue Jul 30 14:04:01 2024

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