Zinc 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:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Aiifl Segment Derived From Alzheimer'S Amyloid-Beta Displayed on 42- Membered Macrocycle Scaffold, PDB code: 3q9j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 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 Zinc with other atoms in the Zn 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 A:Zn12 b:95.9 occ:1.00 O D:ORN10 1.9 82.9 1.0 O A:ORN10 1.9 0.4 1.0 N D:ORN10 2.3 65.2 1.0 N A:ORN10 2.5 50.2 1.0 C D:ORN10 2.7 73.0 1.0 C A:ORN10 2.8 56.7 1.0 CA D:ORN10 3.0 0.9 1.0 CA A:ORN10 3.2 87.5 1.0 N D:ALA1 3.9 81.0 1.0 N A:ALA1 4.0 70.8 1.0 CB D:ORN10 4.0 76.9 1.0 CB A:ORN10 4.3 50.1 1.0 CA D:ALA1 4.7 80.9 1.0 CA A:ALA1 4.7 67.0 1.0 CG D:ORN10 5.0 71.0 1.0

Zinc binding site 2 out of 8 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 Zinc with other atoms in the Zn 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 A:Zn18 b:59.5 occ:1.00 O H:ORN6 2.0 55.3 1.0 N A:ORN6 2.0 54.5 1.0 O A:ORN6 2.0 71.8 1.0 O H:HOH22 2.1 79.2 1.0 N H:ORN6 2.3 53.0 1.0 O H:HOH13 2.6 69.5 1.0 C A:ORN6 2.7 46.0 1.0 C H:ORN6 2.8 49.2 1.0 CA A:ORN6 2.8 48.0 1.0 CA H:ORN6 3.1 55.3 1.0 CB A:ORN6 3.8 44.5 1.0 CB H:ORN6 3.9 62.5 1.0 N8 A:HAO7 4.1 45.6 1.0 N8 H:HAO7 4.1 50.2 1.0 O H:HOH16 4.4 69.4 1.0 CG A:ORN6 4.7 65.8 1.0 N9 H:HAO7 4.8 49.9 1.0 N9 A:HAO7 4.8 52.5 1.0 CG H:ORN6 4.9 49.0 1.0 CZ H:PHE4 4.9 51.6 0.5 CZ A:PHE4 4.9 52.8 0.5

Zinc binding site 3 out of 8 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 Zinc with other atoms in the Zn 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 B:Zn13 b:90.4 occ:1.00 O C:ORN10 2.0 79.9 1.0 O B:ORN10 2.0 72.8 1.0 N B:ORN10 2.4 80.7 1.0 N C:ORN10 2.7 66.2 1.0 C B:ORN10 2.9 71.2 1.0 C C:ORN10 2.9 93.6 1.0 CA B:ORN10 3.2 78.5 1.0 CA C:ORN10 3.3 0.5 1.0 N C:ALA1 4.1 88.9 1.0 N B:ALA1 4.1 69.9 1.0 CB B:ORN10 4.2 0.4 1.0 CB C:ORN10 4.4 73.3 1.0 CA C:ALA1 4.8 87.2 1.0 CA B:ALA1 4.8 67.0 1.0

Zinc binding site 4 out of 8 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 Zinc with other atoms in the Zn 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 B:Zn14 b:61.7 occ:1.00 O B:ORN6 2.0 51.2 1.0 O G:ORN6 2.0 75.1 1.0 N G:ORN6 2.1 42.3 1.0 N B:ORN6 2.2 50.3 1.0 O G:HOH23 2.5 67.3 1.0 O B:HOH12 2.6 71.2 1.0 C B:ORN6 2.8 57.8 1.0 C G:ORN6 2.8 59.2 1.0 CA G:ORN6 3.0 68.7 1.0 CA B:ORN6 3.0 55.9 1.0 CB G:ORN6 3.8 45.0 1.0 CB B:ORN6 3.9 50.6 1.0 O B:HOH18 4.1 90.6 1.0 N8 B:HAO7 4.1 54.4 1.0 N8 G:HAO7 4.1 52.5 1.0 O G:HOH21 4.5 63.2 1.0 O G:HOH17 4.5 81.1 1.0 N9 B:HAO7 4.7 55.0 1.0 CG G:ORN6 4.8 42.0 1.0 N9 G:HAO7 4.8 61.5 1.0 CG B:ORN6 4.8 45.4 1.0 CZ G:PHE4 4.9 52.3 0.5 CZ B:PHE4 4.9 50.3 0.5

Zinc binding site 5 out of 8 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 Zinc with other atoms in the Zn binding site number 5 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:Zn15 b:92.2 occ:1.00 N E:ORN6 2.2 0.7 1.0 O E:ORN6 2.2 86.2 1.0 C E:ORN6 3.0 81.6 1.0 CA E:ORN6 3.1 60.5 1.0 CB E:ORN6 4.0 58.3 1.0 N8 E:HAO7 4.3 76.5 1.0 CG E:ORN6 4.9 1.0 1.0 N9 E:HAO7 5.0 44.3 1.0

Zinc binding site 6 out of 8 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 Zinc with other atoms in the Zn binding site number 6 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:Zn19 b:86.9 occ:1.00 O E:ORN10 2.0 75.8 1.0 O H:ORN10 2.0 64.0 1.0 N E:ORN10 2.3 75.5 1.0 N H:ORN10 2.5 57.8 1.0 C E:ORN10 2.8 83.8 1.0 C H:ORN10 2.9 68.7 1.0 CA E:ORN10 3.1 90.0 1.0 CA H:ORN10 3.2 87.4 1.0 N E:ALA1 4.0 79.2 1.0 N H:ALA1 4.1 69.3 1.0 CB E:ORN10 4.1 0.2 1.0 CB H:ORN10 4.3 77.8 1.0 CA E:ALA1 4.7 77.7 1.0 CA H:ALA1 4.8 66.0 1.0

Zinc binding site 7 out of 8 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 Zinc with other atoms in the Zn binding site number 7 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:Zn16 b:92.6 occ:1.00 O F:HOH14 1.9 86.4 1.0 N F:ORN6 2.1 67.0 1.0 O F:ORN6 2.2 91.4 1.0 C F:ORN6 2.9 78.8 1.0 CA F:ORN6 3.0 68.2 1.0 CB F:ORN6 3.9 70.1 1.0 N8 F:HAO7 4.2 77.9 1.0 CG F:ORN6 4.8 72.7 1.0 N9 F:HAO7 4.9 63.0 1.0

Zinc binding site 8 out of 8 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 Zinc with other atoms in the Zn binding site number 8 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:Zn17 b:93.0 occ:1.00 O F:ORN10 2.0 62.3 1.0 O G:ORN10 2.0 85.7 1.0 N G:ORN10 2.4 58.8 1.0 N F:ORN10 2.5 59.9 1.0 C F:ORN10 2.9 94.0 1.0 C G:ORN10 2.9 68.2 1.0 CA G:ORN10 3.2 92.7 1.0 CA F:ORN10 3.2 1.0 1.0 N F:ALA1 4.1 87.4 1.0 N G:ALA1 4.1 71.7 1.0 CB G:ORN10 4.2 69.9 1.0 CB F:ORN10 4.2 62.5 1.0 CA F:ALA1 4.8 85.9 1.0 CA G:ALA1 4.8 68.4 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