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Chlorine in PDB 3q9i: Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative

Protein crystallography data

The structure of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative, PDB code: 3q9i was solved by C.Liu, M.R.Sawaya, D.Eisenberg, J.S.Nowick, P.Cheng, J.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.60 / 1.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.980, 58.980, 128.511, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 21.8

Other elements in 3q9i:

The structure of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative also contains other interesting chemical elements:

Bromine (Br) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative (pdb code 3q9i). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative, PDB code: 3q9i:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3q9i

Go back to Chlorine Binding Sites List in 3q9i
Chlorine binding site 1 out of 7 in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl11

b:39.9
occ:1.00
 N A:ORN6 3.4 26.6 1.0
O A:HOH53 3.4 55.3 1.0
O22 E:HAO7 3.5 25.9 1.0
N E:LEU8 3.6 27.1 1.0
CB A:ORN6 3.9 27.7 1.0
CB E:LEU8 3.9 26.5 1.0
O E:LEU8 4.0 25.5 1.0
CA A:ORN6 4.1 28.0 1.0
O A:ORN6 4.1 15.5 0.5
CA E:LEU8 4.3 26.3 1.0
C21 E:HAO7 4.4 23.6 1.0
C A:ORN6 4.5 26.8 1.0
C23 E:HAO7 4.5 23.9 1.0
C E:LEU8 4.6 26.7 1.0
CG A:ORN6 4.7 30.9 1.0
CZ A:PHE4 4.8 27.8 1.0
O A:HOH47 4.8 44.0 1.0
O A:HOH13 4.9 32.2 1.0

Chlorine binding site 2 out of 7 in 3q9i

Go back to Chlorine Binding Sites List in 3q9i
Chlorine binding site 2 out of 7 in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl12

b:31.1
occ:1.00
 N D:ORN10 3.1 26.3 1.0
N A:ORN6 3.4 26.6 1.0
CA A:ORN6 3.5 28.0 1.0
O1 D:GOL11 3.6 34.8 1.0
O D:ORN10 3.8 29.2 1.0
CG A:ORN6 3.8 30.9 1.0
CA D:ORN10 3.9 26.6 1.0
NE C:ORN6 3.9 33.2 1.0
C D:ORN10 3.9 28.4 1.0
CD C:ORN6 4.0 39.8 1.0
O A:HOH53 4.1 55.3 1.0
CB C:ALA5 4.1 26.4 1.0
CD A:ORN6 4.2 35.6 1.0
O A:HOH13 4.2 32.2 1.0
C C:ALA5 4.3 28.8 1.0
CB A:ORN6 4.4 27.7 1.0
CA C:ALA5 4.5 26.8 1.0
C A:ORN6 4.7 26.8 1.0
N D:LEU1 4.7 26.4 1.0
C3 D:GOL11 4.8 43.8 1.0
O D:HOH31 4.9 63.7 1.0
O A:ALA5 4.9 23.1 1.0
C1 D:GOL11 4.9 33.9 1.0
O2 D:GOL11 5.0 28.4 1.0
NE A:ORN6 5.0 29.1 1.0

Chlorine binding site 3 out of 7 in 3q9i

Go back to Chlorine Binding Sites List in 3q9i
Chlorine binding site 3 out of 7 in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl12

b:54.0
occ:1.00
 NE D:ORN10 3.2 31.8 1.0
NZ G:LYS9 3.3 45.8 1.0
O D:LEU8 3.7 28.5 1.0
CD G:LYS9 3.8 43.1 1.0
CD D:ORN10 3.8 35.5 1.0
CG D:ORN10 3.9 31.7 1.0
C D:LEU8 4.1 29.2 1.0
CE G:LYS9 4.1 42.5 1.0
CG D:LEU8 4.1 26.8 1.0
CD2 D:LEU8 4.2 29.8 1.0
C D:LYS9 4.2 31.6 1.0
CA D:LYS9 4.3 30.9 1.0
N D:LYS9 4.4 27.4 1.0
CB D:LEU8 4.5 27.1 1.0
CB D:ORN10 4.7 30.7 1.0
CA D:LEU8 5.0 25.0 1.0

Chlorine binding site 4 out of 7 in 3q9i

Go back to Chlorine Binding Sites List in 3q9i
Chlorine binding site 4 out of 7 in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl13

b:63.3
occ:1.00
 NZ G:LYS9 3.0 45.8 1.0
O D:LEU8 3.2 28.5 1.0
O G:HOH13 3.3 35.2 1.0
O22 D:HAO7 3.3 30.9 1.0
N D:LEU8 3.3 28.5 1.0
CE G:LYS9 3.7 42.5 1.0
BR G:4BF3 4.0 29.6 0.7
C D:LEU8 4.0 29.2 1.0
CA D:LEU8 4.1 25.0 1.0
C21 D:HAO7 4.2 31.3 1.0
C23 D:HAO7 4.2 29.7 1.0
CB D:LEU8 4.4 27.1 1.0
O G:HOH12 4.9 31.6 1.0

Chlorine binding site 5 out of 7 in 3q9i

Go back to Chlorine Binding Sites List in 3q9i
Chlorine binding site 5 out of 7 in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl11

b:38.3
occ:1.00
 NZ E:LYS9 3.4 45.7 1.0
CE E:LYS9 4.0 45.3 1.0
CD E:LYS9 4.0 38.1 1.0

Chlorine binding site 6 out of 7 in 3q9i

Go back to Chlorine Binding Sites List in 3q9i
Chlorine binding site 6 out of 7 in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl12

b:39.4
occ:1.00
 NE E:ORN6 3.2 29.0 1.0
CD E:ORN6 3.5 33.6 1.0
CG F:ORN6 3.7 31.9 1.0
CD F:ORN6 3.8 31.9 1.0
C E:ALA5 4.1 27.3 1.0
CA E:ALA5 4.1 25.5 1.0
CG E:ORN6 4.3 36.0 1.0
CB E:ALA5 4.5 23.6 1.0
CB F:ORN6 4.9 31.4 1.0
NE F:ORN6 4.9 25.9 1.0

Chlorine binding site 7 out of 7 in 3q9i

Go back to Chlorine Binding Sites List in 3q9i
Chlorine binding site 7 out of 7 in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl12

b:71.8
occ:1.00
 NE H:ORN10 3.1 35.5 1.0
CA H:LYS9 3.8 32.0 1.0
CD H:ORN10 3.9 40.0 1.0
C H:LYS9 3.9 33.8 1.0
CG H:LEU8 4.2 35.0 1.0
O H:LEU8 4.3 31.0 1.0
CD2 H:LEU8 4.4 37.5 1.0
CG H:ORN10 4.4 38.6 1.0
N H:LYS9 4.4 29.0 1.0
C H:LEU8 4.5 30.9 1.0
CG H:LYS9 4.9 39.5 1.0
CB H:LYS9 4.9 33.4 1.0
CD1 H:LEU8 5.0 32.6 1.0

Reference:

C.Liu, M.R.Sawaya, P.N.Cheng, J.Zheng, J.S.Nowick, D.Eisenberg. Characteristics of Amyloid-Related Oligomers Revealed By Crystal Structures of Macrocyclic Beta-Sheet Mimics. J.Am.Chem.Soc. V. 133 6736 2011.
ISSN: ISSN 0002-7863
PubMed: 21473620
DOI: 10.1021/JA200222N
Page generated: Fri Jul 11 09:20:01 2025

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