Atomistry » Zinc » PDB 3q7f-3qln » 3q9j
Atomistry »
  Zinc »
    PDB 3q7f-3qln »
      3q9j »

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

Protein crystallography data

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

Other elements in 3q9j:

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

Zinc Binding Sites:

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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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 3q9j

Go back to Zinc Binding Sites List in 3q9j
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

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 Dec 16 04:44:58 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy