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Bromine 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:

Chlorine (Cl) 7 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 8 binding sites of Bromine where determined in the Lvffa Segment From Alzheimer'S Amyloid-Beta Displayed on 42-Membered Macrocycle Scaffold, Bromide Derivative, PDB code: 3q9i:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 3q9i

Go back to Bromine Binding Sites List in 3q9i
Bromine binding site 1 out of 8 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 Bromine with other atoms in the Br 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:Br3

b:42.2
occ:0.60
 BR A:4BF3 0.0 42.2 0.6
CZ A:4BF3 1.9 37.8 1.0
CE2 A:4BF3 2.8 35.0 1.0
CE1 A:4BF3 2.8 35.6 1.0
CE2 D:4BF3 3.8 36.2 1.0
CD2 D:4BF3 3.8 33.2 1.0
CE D:LYS9 3.9 45.1 1.0
N A:LEU8 4.1 40.3 1.0
CD2 A:4BF3 4.1 34.6 1.0
CD1 A:4BF3 4.1 31.2 1.0
O A:LEU8 4.2 42.7 1.0
CZ D:4BF3 4.2 35.9 1.0
C23 A:HAO7 4.2 35.3 1.0
CG D:4BF3 4.2 26.1 1.0
O22 A:HAO7 4.3 34.4 1.0
C21 A:HAO7 4.3 34.7 1.0
C A:LEU8 4.4 42.9 1.0
CD D:LYS9 4.4 41.4 1.0
CD1 C:LEU1 4.4 30.6 1.0
CB A:LYS9 4.5 45.6 1.0
O D:HOH30 4.5 56.6 1.0
CE1 D:4BF3 4.6 30.4 1.0
CD1 D:4BF3 4.6 30.4 1.0
CG A:4BF3 4.6 30.8 1.0
N A:LYS9 4.8 43.0 1.0
CA A:LEU8 4.9 42.3 1.0
NZ D:LYS9 4.9 43.8 1.0
N20 A:HAO7 4.9 26.5 1.0
CB D:4BF3 5.0 24.3 1.0

Bromine binding site 2 out of 8 in 3q9i

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Bromine binding site 2 out of 8 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 Bromine with other atoms in the Br 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
B:Br3

b:46.7
occ:0.55
 BR B:4BF3 0.0 46.7 0.6
CZ B:4BF3 1.9 41.8 1.0
CE1 B:4BF3 2.8 39.3 1.0
CE2 B:4BF3 2.9 37.1 1.0
O22 B:HAO7 3.8 43.2 1.0
NZ C:LYS9 3.8 46.8 1.0
C21 B:HAO7 4.1 39.2 1.0
CD1 B:4BF3 4.2 36.9 1.0
CD2 B:4BF3 4.2 37.0 1.0
N B:LEU8 4.2 38.5 1.0
C23 B:HAO7 4.3 38.1 1.0
O B:LEU8 4.3 38.5 1.0
O F:HOH35 4.7 51.3 1.0
CE C:LYS9 4.7 47.5 1.0
CG B:4BF3 4.7 33.7 1.0
C B:LEU8 4.7 38.9 1.0
N20 B:HAO7 4.8 35.6 1.0

Bromine binding site 3 out of 8 in 3q9i

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Bromine binding site 3 out of 8 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 Bromine with other atoms in the Br 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
C:Br3

b:41.3
occ:0.60
 BR C:4BF3 0.0 41.3 0.6
CZ C:4BF3 1.9 37.4 1.0
CE1 C:4BF3 2.8 33.1 1.0
CE2 C:4BF3 2.8 29.0 1.0
O B:LYS9 3.5 38.2 1.0
CG B:LYS9 3.6 42.9 1.0
CD B:LYS9 3.7 43.1 1.0
O C:HOH37 3.9 50.0 1.0
O22 C:HAO7 3.9 37.8 1.0
CB B:LEU1 3.9 31.9 1.0
N C:LEU8 4.0 36.4 1.0
C21 C:HAO7 4.0 37.1 1.0
C23 C:HAO7 4.1 34.8 1.0
CB B:LYS9 4.1 40.6 1.0
CD1 C:4BF3 4.1 30.2 1.0
CE B:LYS9 4.1 47.1 1.0
CD2 C:4BF3 4.1 32.2 1.0
O C:LEU8 4.2 36.0 1.0
C B:LYS9 4.5 39.4 1.0
CD2 B:LEU1 4.6 35.0 1.0
C C:LEU8 4.6 37.8 1.0
N20 C:HAO7 4.6 29.8 1.0
CG C:4BF3 4.6 28.2 1.0
N B:LEU1 4.6 31.9 1.0
CG B:LEU1 4.9 33.5 1.0
CA C:LEU8 4.9 37.8 1.0
CA B:LYS9 4.9 38.0 1.0
NZ B:LYS9 4.9 39.8 1.0
O24 C:HAO7 4.9 25.4 1.0
CA B:LEU1 4.9 29.6 1.0

Bromine binding site 4 out of 8 in 3q9i

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Bromine binding site 4 out of 8 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 Bromine with other atoms in the Br 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:Br3

b:47.5
occ:0.80
 BR D:4BF3 0.0 47.5 0.8
CZ D:4BF3 1.9 35.9 1.0
CE1 D:4BF3 2.9 30.4 1.0
CE2 D:4BF3 2.9 36.2 1.0
O D:HOH30 3.9 56.6 1.0
CE D:LYS9 3.9 45.1 1.0
O22 D:HAO7 3.9 30.9 1.0
CD1 D:4BF3 4.2 30.4 1.0
CD2 D:4BF3 4.2 33.2 1.0
C21 D:HAO7 4.2 31.3 1.0
C13 D:HAO7 4.4 27.6 1.0
N20 D:HAO7 4.5 28.7 1.0
C19 D:HAO7 4.6 28.7 1.0
CG D:4BF3 4.7 26.1 1.0
O A:HOH48 4.8 45.3 1.0
C23 D:HAO7 4.8 29.7 1.0
NZ D:LYS9 4.8 43.8 1.0
CD D:LYS9 4.9 41.4 1.0

Bromine binding site 5 out of 8 in 3q9i

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Bromine binding site 5 out of 8 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 Bromine with other atoms in the Br 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:Br3

b:24.7
occ:0.65
 BR E:4BF3 0.0 24.7 0.7
CZ E:4BF3 1.8 24.9 1.0
CE1 E:4BF3 2.8 26.5 1.0
CE2 E:4BF3 2.8 23.6 1.0
O E:ALA5 3.8 25.7 1.0
CB E:ALA5 3.9 23.6 1.0
CD1 E:4BF3 4.1 25.6 1.0
C E:ALA5 4.1 27.3 1.0
CD2 E:4BF3 4.1 23.5 1.0
CA E:ALA5 4.6 25.5 1.0
CG E:4BF3 4.6 24.4 1.0
NE E:ORN6 4.6 29.0 1.0

Bromine binding site 6 out of 8 in 3q9i

Go back to Bromine Binding Sites List in 3q9i
Bromine binding site 6 out of 8 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 Bromine with other atoms in the Br 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
F:Br3

b:35.3
occ:0.65
 BR F:4BF3 0.0 35.3 0.7
CZ F:4BF3 1.9 35.8 1.0
CE1 F:4BF3 2.8 32.0 1.0
CE2 F:4BF3 2.9 33.1 1.0
O22 B:HAO7 3.7 43.2 1.0
O22 F:HAO7 3.7 29.9 1.0
O F:HOH35 3.8 51.3 1.0
O F:LEU8 3.9 32.4 1.0
N F:LEU8 3.9 32.6 1.0
C21 F:HAO7 4.0 35.8 1.0
C23 F:HAO7 4.0 31.2 1.0
C21 B:HAO7 4.1 39.2 1.0
N B:LEU8 4.1 38.5 1.0
CD1 F:4BF3 4.1 28.2 1.0
CD2 F:4BF3 4.2 27.2 1.0
CB B:LEU8 4.2 35.7 1.0
C F:LEU8 4.3 32.6 1.0
C23 B:HAO7 4.3 38.1 1.0
CA F:LEU8 4.6 32.0 1.0
CE F:LYS9 4.6 55.2 1.0
CG F:4BF3 4.7 27.0 1.0
C18 B:HAO7 4.7 45.9 1.0
N20 F:HAO7 4.8 27.8 1.0
CA B:LEU8 4.8 37.0 1.0
N20 B:HAO7 4.8 35.6 1.0
CB F:LYS9 5.0 37.4 1.0
N F:LYS9 5.0 33.0 1.0

Bromine binding site 7 out of 8 in 3q9i

Go back to Bromine Binding Sites List in 3q9i
Bromine binding site 7 out of 8 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 Bromine with other atoms in the Br 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
G:Br3

b:29.6
occ:0.70
 BR G:4BF3 0.0 29.6 0.7
CZ G:4BF3 1.9 30.3 1.0
CE2 G:4BF3 2.9 27.4 1.0
CE1 G:4BF3 2.9 30.6 1.0
O G:HOH13 3.3 35.2 1.0
O22 D:HAO7 3.7 30.9 1.0
O G:HOH12 3.7 31.6 1.0
N G:LEU8 3.8 30.4 1.0
O G:LEU8 3.8 29.7 1.0
O22 G:HAO7 3.9 26.5 1.0
N D:LEU8 4.0 28.5 1.0
CL D:CL13 4.0 63.3 1.0
C21 G:HAO7 4.1 30.6 1.0
C23 G:HAO7 4.1 29.6 1.0
C21 D:HAO7 4.1 31.3 1.0
C G:LEU8 4.2 29.6 1.0
CD1 G:4BF3 4.2 27.6 1.0
CD2 G:4BF3 4.2 24.1 1.0
CB D:LEU8 4.2 27.1 1.0
C23 D:HAO7 4.3 29.7 1.0
O G:HOH31 4.4 38.5 1.0
CA G:LEU8 4.4 29.3 1.0
CE G:LYS9 4.5 42.5 1.0
CB G:LYS9 4.7 31.0 1.0
CG G:4BF3 4.7 23.9 1.0
CA D:LEU8 4.8 25.0 1.0
C18 D:HAO7 4.8 31.9 1.0
N G:LYS9 4.8 29.2 1.0
N20 G:HAO7 4.9 25.4 1.0
N20 D:HAO7 4.9 28.7 1.0

Bromine binding site 8 out of 8 in 3q9i

Go back to Bromine Binding Sites List in 3q9i
Bromine binding site 8 out of 8 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 Bromine with other atoms in the Br binding site number 8 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:Br3

b:26.7
occ:0.80
 BR H:4BF3 0.0 26.7 0.8
CZ H:4BF3 1.9 25.9 1.0
CE1 H:4BF3 2.8 27.6 1.0
CE2 H:4BF3 2.8 23.6 1.0
CB H:ALA5 3.9 22.2 1.0
O H:ALA5 4.0 23.3 1.0
CD1 H:4BF3 4.1 25.4 1.0
CD2 H:4BF3 4.1 22.2 1.0
C H:ALA5 4.3 23.3 1.0
CG H:4BF3 4.6 21.9 1.0
CA H:ALA5 4.6 23.6 1.0
NE H:ORN6 4.8 26.8 1.0
CE2 G:PHE4 4.8 28.2 1.0
CD2 G:PHE4 5.0 27.9 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: Wed Jul 10 20:13:43 2024

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