Chlorine in PDB 3q9j: Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold

The structure of Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold, PDB code: 3q9j 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)	18.18 / 2.55
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	41.780, 41.780, 63.060, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 22.3

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

Zinc

(Zn)

8 atoms

The binding sites of Chlorine atom in the Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold (pdb code 3q9j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold, PDB code: 3q9j:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl11 b:0.8 occ:1.00 NZ C:LYS9 3.1 0.5 1.0 CD A:LYS9 4.0 0.1 1.0 CB C:LEU5 4.0 59.3 1.0 O11 C:HAO7 4.0 63.7 1.0 CG1 C:ILE3 4.1 71.5 1.0 CE C:LYS9 4.2 0.7 1.0 CE A:LYS9 4.3 0.5 1.0 CG2 C:ILE3 4.4 73.1 1.0 NZ A:LYS9 4.4 94.0 1.0 N C:LEU5 4.5 62.5 1.0 CD2 C:LEU5 4.7 65.5 1.0 CD1 C:ILE3 4.8 74.4 1.0 O C:ILE3 4.8 73.9 1.0 C13 C:HAO7 4.8 0.8 1.0 CB C:ILE3 4.9 73.2 1.0 CA C:LEU5 4.9 59.9 1.0 C10 C:HAO7 4.9 83.1 1.0

Chlorine binding site 2 out of 4 in the Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl11 b:0.7 occ:1.00 NZ D:LYS9 2.7 0.9 1.0 CE D:LYS9 3.7 0.1 1.0 CD B:LYS9 4.1 1.0 1.0 CE B:LYS9 4.2 0.1 1.0 O11 D:HAO7 4.2 65.7 1.0 CG2 D:ILE3 4.2 67.6 1.0 NZ B:LYS9 4.3 0.6 1.0 CG1 D:ILE3 4.3 64.1 1.0 CB D:LEU5 4.4 66.3 1.0 C13 D:HAO7 4.7 93.8 1.0 O D:ILE3 4.8 67.9 1.0 CD D:LYS9 4.9 0.2 1.0 N D:LEU5 4.9 67.3 1.0 CB D:ILE3 4.9 66.1 1.0 CD2 D:LEU5 5.0 74.6 1.0

Chlorine binding site 3 out of 4 in the Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl11 b:0.5 occ:1.00 NZ E:LYS9 2.9 0.6 1.0 CE E:LYS9 3.5 0.5 1.0 CE G:LYS9 4.1 0.6 1.0 NZ G:LYS9 4.1 0.8 1.0 O11 E:HAO7 4.2 57.5 1.0 CD G:LYS9 4.2 0.9 1.0 C13 E:HAO7 4.4 78.2 1.0 CG2 E:ILE3 4.7 72.7 1.0 C10 E:HAO7 4.8 95.5 1.0 CD E:LYS9 4.8 0.3 1.0 O E:ILE3 4.9 73.2 1.0 C12 E:HAO7 4.9 51.4 1.0

Chlorine binding site 4 out of 4 in the Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl11 b:0.0 occ:1.00 NZ F:LYS9 2.6 0.5 1.0 CE F:LYS9 3.7 0.9 1.0 CG2 F:ILE3 4.0 70.9 1.0 CG1 F:ILE3 4.0 67.2 1.0 CD H:LYS9 4.2 0.6 1.0 CB F:LEU5 4.3 67.0 1.0 CE H:LYS9 4.4 0.2 1.0 O11 F:HAO7 4.6 77.4 1.0 CB F:ILE3 4.6 69.2 1.0 CD1 F:ILE3 4.6 73.4 1.0 CD F:LYS9 4.7 0.6 1.0 CD2 F:LEU5 4.8 73.5 1.0 O F:ILE3 4.8 72.2 1.0 NZ H:LYS9 4.9 0.5 1.0 N F:LEU5 4.9 67.6 1.0

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