Atomistry » Zinc » PDB 5yho-5ynp » 5yj0
Atomistry »
  Zinc »
    PDB 5yho-5ynp »
      5yj0 »

Zinc in PDB 5yj0: Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide

Protein crystallography data

The structure of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide, PDB code: 5yj0 was solved by T.Mori, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.15 / 1.80
Space group H 3 1
Cell size a, b, c (Å), α, β, γ (°) 201.897, 201.897, 123.614, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 20.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide (pdb code 5yj0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide, PDB code: 5yj0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 1 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:36.9
occ:1.00
 SG A:CYS329 2.3 34.2 1.0
SG A:CYS394 2.3 29.5 1.0
SG A:CYS326 2.3 26.0 1.0
SG A:CYS397 2.3 29.4 1.0
CB A:CYS394 3.3 28.0 1.0
CB A:CYS329 3.3 35.9 1.0
CB A:CYS326 3.3 31.8 1.0
CB A:CYS397 3.4 36.8 1.0
N A:CYS329 3.8 37.6 1.0
N A:CYS397 3.8 32.8 1.0
OG1 A:THR332 4.1 35.9 1.0
CA A:CYS329 4.1 35.2 1.0
CA A:CYS397 4.2 32.7 1.0
CB A:ILE396 4.5 33.7 1.0
CB A:SER399 4.7 34.1 1.0
CB A:GLN328 4.7 30.2 1.0
CA A:CYS394 4.7 30.0 1.0
CA A:CYS326 4.7 27.9 1.0
C A:CYS397 4.8 35.0 1.0
C A:GLN328 4.9 41.8 1.0
N A:GLN330 4.9 34.5 1.0
C A:CYS329 4.9 37.3 1.0
C A:ILE396 4.9 37.7 1.0
N A:ALA398 4.9 30.2 1.0
CG2 A:ILE396 5.0 35.9 1.0

Zinc binding site 2 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 2 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:36.5
occ:1.00
 SG D:CYS394 2.3 28.2 1.0
SG D:CYS326 2.3 26.3 1.0
SG D:CYS397 2.3 30.8 1.0
SG D:CYS329 2.3 33.0 1.0
CB D:CYS394 3.2 28.5 1.0
CB D:CYS329 3.3 34.7 1.0
CB D:CYS326 3.3 31.8 1.0
CB D:CYS397 3.3 37.4 1.0
N D:CYS397 3.8 33.4 1.0
N D:CYS329 3.8 38.0 1.0
OG1 D:THR332 4.1 35.8 1.0
CA D:CYS329 4.1 35.6 1.0
CA D:CYS397 4.1 32.9 1.0
CB D:ILE396 4.5 33.5 1.0
CB D:SER399 4.7 30.9 1.0
CA D:CYS394 4.7 29.8 1.0
CA D:CYS326 4.7 27.9 1.0
CB D:GLN328 4.8 31.0 1.0
C D:CYS397 4.8 35.2 1.0
C D:ILE396 4.9 37.5 1.0
N D:ALA398 4.9 30.8 1.0
C D:GLN328 4.9 42.3 1.0
N D:GLN330 4.9 31.7 1.0
C D:CYS329 4.9 37.2 1.0

Zinc binding site 3 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 3 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn502

b:36.4
occ:1.00
 SG G:CYS329 2.3 31.7 1.0
SG G:CYS394 2.3 29.0 1.0
SG G:CYS326 2.3 27.3 1.0
SG G:CYS397 2.3 30.6 1.0
CB G:CYS394 3.2 26.9 1.0
CB G:CYS326 3.3 30.9 1.0
CB G:CYS329 3.3 31.2 1.0
CB G:CYS397 3.4 37.7 1.0
N G:CYS397 3.8 32.0 1.0
N G:CYS329 3.9 35.9 1.0
OG1 G:THR332 4.1 32.8 1.0
CA G:CYS329 4.2 33.6 1.0
CA G:CYS397 4.2 31.3 1.0
CB G:ILE396 4.5 32.6 1.0
CB G:SER399 4.7 33.0 1.0
CB G:GLN328 4.7 31.6 1.0
CA G:CYS394 4.7 27.5 1.0
CA G:CYS326 4.7 28.1 1.0
C G:CYS397 4.8 32.8 1.0
C G:GLN328 4.8 40.2 1.0
N G:GLN330 4.9 32.1 1.0
C G:CYS329 4.9 36.8 1.0
C G:ILE396 4.9 35.5 1.0
N G:ALA398 4.9 28.8 1.0
CG2 G:ILE396 5.0 33.3 1.0

Zinc binding site 4 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 4 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn502

b:25.4
occ:1.00
 SG J:CYS329 2.3 20.5 1.0
SG J:CYS394 2.3 18.9 1.0
SG J:CYS397 2.3 19.2 1.0
SG J:CYS326 2.3 19.6 1.0
CB J:CYS326 3.2 18.0 1.0
CB J:CYS394 3.2 17.8 1.0
CB J:CYS329 3.3 23.1 1.0
CB J:CYS397 3.4 23.0 1.0
N J:CYS329 3.8 22.2 1.0
N J:CYS397 3.9 16.6 1.0
CA J:CYS329 4.1 20.5 1.0
CA J:CYS397 4.2 19.1 1.0
CB J:ILE396 4.5 23.6 1.0
CA J:CYS326 4.6 19.3 1.0
OG1 J:THR332 4.6 22.2 1.0
CB J:THR332 4.6 21.4 1.0
CB J:GLN328 4.6 19.1 1.0
CA J:CYS394 4.7 16.4 1.0
OG J:SER399 4.8 26.0 1.0
CB J:SER399 4.8 22.7 1.0
C J:GLN328 4.9 25.2 1.0
C J:ILE396 4.9 24.3 1.0
C J:CYS397 4.9 23.3 1.0
C J:CYS326 5.0 19.5 1.0
C J:CYS329 5.0 21.6 1.0
CG2 J:ILE396 5.0 23.3 1.0

Zinc binding site 5 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 5 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn502

b:30.7
occ:1.00
 SG M:CYS394 2.3 22.1 1.0
SG M:CYS329 2.3 26.7 1.0
SG M:CYS397 2.3 23.9 1.0
SG M:CYS326 2.3 23.6 1.0
CB M:CYS394 3.2 24.1 1.0
CB M:CYS326 3.2 20.9 1.0
CB M:CYS329 3.3 31.5 1.0
CB M:CYS397 3.4 25.3 1.0
N M:CYS329 3.7 28.1 1.0
N M:CYS397 3.9 26.4 1.0
CA M:CYS329 4.1 27.1 1.0
CA M:CYS397 4.2 25.8 1.0
CB M:ILE396 4.4 29.0 1.0
OG1 M:THR332 4.6 25.6 1.0
CB M:GLN328 4.6 25.0 1.0
CA M:CYS326 4.7 21.5 1.0
CA M:CYS394 4.7 25.1 1.0
CB M:THR332 4.7 27.1 1.0
CB M:SER399 4.8 31.0 1.0
C M:GLN328 4.8 30.0 1.0
C M:ILE396 4.8 30.7 1.0
CG2 M:ILE396 4.9 31.8 1.0
C M:CYS397 4.9 29.0 1.0
C M:CYS329 5.0 28.7 1.0

Zinc binding site 6 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 6 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn502

b:27.0
occ:1.00
 SG P:CYS394 2.3 20.8 1.0
SG P:CYS326 2.3 22.0 1.0
SG P:CYS329 2.3 22.1 1.0
SG P:CYS397 2.3 21.7 1.0
CB P:CYS394 3.2 19.6 1.0
CB P:CYS326 3.2 19.5 1.0
CB P:CYS329 3.2 22.0 1.0
CB P:CYS397 3.4 23.3 1.0
N P:CYS329 3.8 22.6 1.0
N P:CYS397 3.8 22.5 1.0
CA P:CYS329 4.1 20.3 1.0
CA P:CYS397 4.1 22.2 1.0
CB P:ILE396 4.5 20.9 1.0
CB P:SER399 4.6 23.2 1.0
OG1 P:THR332 4.6 25.1 1.0
CB P:THR332 4.6 26.4 1.0
CA P:CYS394 4.7 21.2 1.0
CA P:CYS326 4.7 18.6 1.0
CB P:GLN328 4.7 22.1 1.0
C P:ILE396 4.7 25.5 1.0
C P:CYS397 4.8 26.6 1.0
C P:GLN328 4.9 21.9 1.0
N P:ALA398 4.9 24.0 1.0
C P:CYS329 4.9 20.5 1.0
N P:SER399 5.0 20.4 1.0
N P:ILE396 5.0 20.2 1.0
CA P:ILE396 5.0 21.4 1.0

Zinc binding site 7 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 7 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn502

b:27.4
occ:1.00
 SG S:CYS329 2.3 21.9 1.0
SG S:CYS394 2.3 20.4 1.0
SG S:CYS326 2.3 21.6 1.0
SG S:CYS397 2.3 21.4 1.0
CB S:CYS394 3.2 20.9 1.0
CB S:CYS326 3.2 18.6 1.0
CB S:CYS329 3.3 21.7 1.0
CB S:CYS397 3.4 22.2 1.0
N S:CYS329 3.8 24.0 1.0
N S:CYS397 3.8 22.8 1.0
CA S:CYS329 4.1 22.0 1.0
CA S:CYS397 4.1 23.4 1.0
CB S:ILE396 4.5 20.3 1.0
CB S:SER399 4.5 23.9 1.0
OG1 S:THR332 4.6 23.8 1.0
CB S:THR332 4.6 24.5 1.0
CB S:GLN328 4.6 21.1 1.0
CA S:CYS394 4.7 21.1 1.0
CA S:CYS326 4.7 17.9 1.0
C S:CYS397 4.7 25.4 1.0
C S:ILE396 4.8 24.3 1.0
C S:GLN328 4.9 23.0 1.0
N S:ALA398 4.9 23.4 1.0
N S:SER399 4.9 21.6 1.0
C S:CYS329 5.0 21.6 1.0
N S:ILE396 5.0 19.9 1.0
CG2 S:ILE396 5.0 24.7 1.0
CA S:ILE396 5.0 21.5 1.0

Zinc binding site 8 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 8 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn502

b:26.0
occ:1.00
 SG V:CYS329 2.3 20.5 1.0
SG V:CYS394 2.3 18.1 1.0
SG V:CYS397 2.3 19.2 1.0
SG V:CYS326 2.3 19.9 1.0
CB V:CYS326 3.2 18.4 1.0
CB V:CYS394 3.2 17.1 1.0
CB V:CYS329 3.3 20.6 1.0
CB V:CYS397 3.4 23.7 1.0
N V:CYS329 3.8 22.6 1.0
N V:CYS397 3.9 17.5 1.0
CA V:CYS329 4.1 19.3 1.0
CA V:CYS397 4.2 19.8 1.0
CB V:ILE396 4.5 22.4 1.0
OG1 V:THR332 4.6 20.3 1.0
CA V:CYS326 4.6 19.7 1.0
CB V:THR332 4.6 19.9 1.0
CB V:GLN328 4.6 20.5 1.0
CA V:CYS394 4.7 15.8 1.0
OG V:SER399 4.8 25.9 1.0
CB V:SER399 4.8 23.4 1.0
C V:GLN328 4.9 24.1 1.0
C V:ILE396 4.9 24.5 1.0
C V:CYS397 4.9 23.6 1.0
C V:CYS326 4.9 19.4 1.0

Zinc binding site 9 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 9 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn502

b:30.6
occ:1.00
 SG Y:CYS329 2.3 27.5 1.0
SG Y:CYS394 2.3 22.9 1.0
SG Y:CYS397 2.3 23.6 1.0
SG Y:CYS326 2.3 24.2 1.0
CB Y:CYS394 3.2 24.6 1.0
CB Y:CYS326 3.2 22.5 1.0
CB Y:CYS329 3.3 31.6 1.0
CB Y:CYS397 3.4 26.9 1.0
N Y:CYS329 3.7 29.2 1.0
N Y:CYS397 3.8 26.3 1.0
CA Y:CYS329 4.1 26.4 1.0
CA Y:CYS397 4.2 27.6 1.0
CB Y:ILE396 4.4 27.9 1.0
OG1 Y:THR332 4.5 27.5 1.0
CB Y:GLN328 4.6 23.3 1.0
CA Y:CYS394 4.7 26.0 1.0
CB Y:THR332 4.7 27.4 1.0
CA Y:CYS326 4.7 24.4 1.0
C Y:GLN328 4.8 29.7 1.0
CG2 Y:ILE396 4.8 33.4 1.0
C Y:ILE396 4.8 30.6 1.0
C Y:CYS397 4.9 29.4 1.0
CB Y:SER399 4.9 30.0 1.0
C Y:CYS329 5.0 27.2 1.0
N Y:ALA398 5.0 24.0 1.0

Zinc binding site 10 out of 16 in 5yj0

Go back to Zinc Binding Sites List in 5yj0
Zinc binding site 10 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Mouse Cereblon Thalidomide Binding Domain Complexed with S-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Zn502

b:27.4
occ:1.00
 SG b:CYS394 2.3 20.7 1.0
SG b:CYS329 2.3 21.6 1.0
SG b:CYS326 2.3 21.8 1.0
SG b:CYS397 2.3 22.4 1.0
CB b:CYS394 3.2 20.8 1.0
CB b:CYS326 3.2 18.7 1.0
CB b:CYS329 3.3 23.6 1.0
CB b:CYS397 3.4 22.7 1.0
N b:CYS329 3.8 22.6 1.0
N b:CYS397 3.8 22.5 1.0
CA b:CYS329 4.1 22.2 1.0
CA b:CYS397 4.1 22.9 1.0
CB b:SER399 4.5 23.2 1.0
CB b:ILE396 4.5 21.2 1.0
OG1 b:THR332 4.6 23.1 1.0
CB b:THR332 4.6 24.9 1.0
CB b:GLN328 4.6 20.8 1.0
CA b:CYS394 4.6 20.8 1.0
CA b:CYS326 4.7 19.4 1.0
C b:CYS397 4.8 26.4 1.0
C b:ILE396 4.8 25.6 1.0
C b:GLN328 4.8 22.1 1.0
N b:ALA398 4.9 23.0 1.0
N b:SER399 4.9 20.5 1.0
C b:CYS329 5.0 20.4 1.0
N b:ILE396 5.0 20.3 1.0

Reference:

T.Mori, T.Ito, S.Liu, H.Ando, S.Sakamoto, Y.Yamaguchi, E.Tokunaga, N.Shibata, H.Handa, T.Hakoshima. Structural Basis of Thalidomide Enantiomer Binding to Cereblon Sci Rep V. 8 1294 2018.
ISSN: ESSN 2045-2322
PubMed: 29358579
DOI: 10.1038/S41598-018-19202-7
Page generated: Mon Oct 28 15:47:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy