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Zinc in PDB 5yj1: Mouse Cereblon Thalidomide Binding Domain Complexed with R-Form Thalidomide

Protein crystallography data

The structure of Mouse Cereblon Thalidomide Binding Domain Complexed with R-Form Thalidomide, PDB code: 5yj1 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) 19.78 / 2.00
Space group H 3 1
Cell size a, b, c (Å), α, β, γ (°) 201.615, 201.615, 123.572, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 22.8

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 R-Form Thalidomide (pdb code 5yj1). 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 R-Form Thalidomide, PDB code: 5yj1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 5yj1

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Zinc binding site 1 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:46.3
occ:1.00
 SG A:CYS329 2.3 39.4 1.0
SG A:CYS397 2.3 35.7 1.0
SG A:CYS394 2.3 32.0 1.0
SG A:CYS326 2.3 28.4 1.0
CB A:CYS394 3.2 33.1 1.0
CB A:CYS329 3.3 44.5 1.0
CB A:CYS326 3.3 35.5 1.0
CB A:CYS397 3.4 40.1 1.0
N A:CYS397 3.8 37.1 1.0
N A:CYS329 3.9 42.6 1.0
OG1 A:THR332 4.1 43.9 1.0
CA A:CYS397 4.1 37.1 1.0
CA A:CYS329 4.1 41.0 1.0
CB A:ILE396 4.5 37.5 1.0
CB A:GLN328 4.7 36.9 1.0
CA A:CYS394 4.7 33.0 1.0
CB A:SER399 4.7 32.6 1.0
CA A:CYS326 4.8 33.9 1.0
C A:CYS397 4.8 38.8 1.0
C A:ILE396 4.8 37.7 1.0
C A:GLN328 4.9 42.7 1.0
N A:ALA398 4.9 33.7 1.0
C A:CYS329 5.0 42.5 1.0
N A:GLN330 5.0 40.2 1.0

Zinc binding site 2 out of 16 in 5yj1

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Zinc binding site 2 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:45.5
occ:1.00
 SG D:CYS394 2.3 32.6 1.0
SG D:CYS397 2.3 34.4 1.0
SG D:CYS329 2.4 43.1 1.0
SG D:CYS326 2.5 29.4 1.0
CB D:CYS329 2.7 44.3 1.0
CB D:CYS394 3.2 36.0 1.0
CB D:CYS397 3.4 41.3 1.0
N D:CYS329 3.5 43.2 1.0
CB D:CYS326 3.7 36.1 1.0
CA D:CYS329 3.7 42.9 1.0
N D:CYS397 3.9 37.8 1.0
CA D:CYS397 4.2 37.2 1.0
OG1 D:THR332 4.2 47.5 1.0
CB D:ILE396 4.6 38.0 1.0
CB D:SER399 4.6 31.4 1.0
CA D:CYS394 4.6 34.5 1.0
CB D:GLN328 4.7 37.6 1.0
C D:GLN328 4.7 46.0 1.0
C D:CYS329 4.7 45.3 1.0
C D:CYS397 4.8 39.3 1.0
N D:GLN330 4.8 43.2 1.0
C D:ILE396 4.9 37.9 1.0
N D:ALA398 4.9 36.5 1.0

Zinc binding site 3 out of 16 in 5yj1

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Zinc binding site 3 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn502

b:46.4
occ:1.00
 SG G:CYS329 2.3 35.9 1.0
SG G:CYS326 2.3 28.6 1.0
SG G:CYS394 2.3 32.8 1.0
SG G:CYS397 2.3 35.1 1.0
CB G:CYS394 3.3 33.2 1.0
CB G:CYS329 3.3 39.9 1.0
CB G:CYS326 3.3 35.0 1.0
CB G:CYS397 3.4 38.9 1.0
N G:CYS329 3.8 41.2 1.0
N G:CYS397 3.9 35.7 1.0
OG1 G:THR332 4.0 45.4 1.0
CA G:CYS329 4.1 38.1 1.0
CA G:CYS397 4.2 36.4 1.0
CB G:ILE396 4.5 36.6 1.0
CB G:GLN328 4.5 38.6 1.0
CA G:CYS394 4.7 32.5 1.0
CA G:CYS326 4.7 32.9 1.0
CB G:SER399 4.8 31.5 1.0
N G:GLN330 4.8 38.2 1.0
C G:CYS397 4.9 39.1 1.0
C G:CYS329 4.9 40.5 1.0
C G:ILE396 4.9 36.1 1.0
CG2 G:ILE396 4.9 34.2 1.0
C G:GLN328 4.9 42.9 1.0
N G:ALA398 5.0 33.7 1.0
C G:CYS326 5.0 34.6 1.0

Zinc binding site 4 out of 16 in 5yj1

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Zinc binding site 4 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn502

b:33.8
occ:1.00
 SG J:CYS329 2.3 23.6 1.0
SG J:CYS394 2.3 23.8 1.0
SG J:CYS326 2.3 22.3 1.0
SG J:CYS397 2.3 21.6 1.0
CB J:CYS326 3.2 19.2 1.0
CB J:CYS394 3.2 19.8 1.0
CB J:CYS329 3.3 23.8 1.0
CB J:CYS397 3.4 22.7 1.0
N J:CYS329 3.7 25.7 1.0
N J:CYS397 3.9 23.5 1.0
CA J:CYS329 4.1 24.7 1.0
CA J:CYS397 4.2 21.4 1.0
CB J:ILE396 4.5 28.9 1.0
CB J:GLN328 4.5 22.6 1.0
OG1 J:THR332 4.6 25.6 1.0
CB J:THR332 4.6 25.7 1.0
CA J:CYS326 4.6 21.5 1.0
CA J:CYS394 4.7 19.4 1.0
OG J:SER399 4.8 35.6 1.0
CB J:SER399 4.8 25.1 1.0
C J:GLN328 4.8 24.8 1.0
C J:ILE396 4.8 28.0 1.0
C J:CYS326 4.9 22.6 1.0
C J:CYS397 4.9 26.0 1.0
CG2 J:ILE396 4.9 29.3 1.0
C J:CYS329 5.0 23.5 1.0

Zinc binding site 5 out of 16 in 5yj1

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Zinc binding site 5 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn502

b:39.3
occ:1.00
 SG M:CYS394 2.3 33.6 1.0
SG M:CYS329 2.3 29.5 1.0
SG M:CYS397 2.3 28.7 1.0
SG M:CYS326 2.3 27.8 1.0
CB M:CYS394 3.2 34.4 1.0
CB M:CYS326 3.3 25.1 1.0
CB M:CYS329 3.3 32.0 1.0
CB M:CYS397 3.4 29.2 1.0
N M:CYS329 3.7 30.5 1.0
N M:CYS397 3.8 33.1 1.0
CA M:CYS329 4.1 31.2 1.0
CA M:CYS397 4.2 29.2 1.0
CB M:ILE396 4.4 36.3 1.0
CB M:GLN328 4.6 26.6 1.0
OG1 M:THR332 4.6 29.2 1.0
CG2 M:ILE396 4.7 38.9 1.0
CB M:THR332 4.7 31.0 1.0
CA M:CYS394 4.7 30.9 1.0
CA M:CYS326 4.7 26.2 1.0
C M:GLN328 4.7 32.1 1.0
OG M:SER399 4.8 43.5 1.0
C M:ILE396 4.8 34.6 1.0
C M:CYS397 4.9 31.1 1.0
C M:CYS329 4.9 31.7 1.0
CA M:GLN328 5.0 28.6 1.0
N M:GLN328 5.0 28.6 1.0

Zinc binding site 6 out of 16 in 5yj1

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Zinc binding site 6 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn502

b:36.2
occ:1.00
 SG P:CYS394 2.3 24.7 1.0
SG P:CYS326 2.3 26.3 1.0
SG P:CYS329 2.3 25.2 1.0
SG P:CYS397 2.4 24.1 1.0
CB P:CYS394 3.2 24.1 1.0
CB P:CYS326 3.3 24.8 1.0
CB P:CYS329 3.3 26.4 1.0
CB P:CYS397 3.4 24.1 1.0
N P:CYS329 3.7 26.8 1.0
N P:CYS397 3.8 27.7 1.0
CA P:CYS329 4.1 25.3 1.0
CA P:CYS397 4.1 28.4 1.0
CB P:ILE396 4.5 28.7 1.0
CB P:SER399 4.5 25.7 1.0
OG1 P:THR332 4.6 28.1 1.0
CB P:GLN328 4.6 22.9 1.0
CB P:THR332 4.6 27.3 1.0
CA P:CYS394 4.6 26.0 1.0
CA P:CYS326 4.7 22.7 1.0
C P:ILE396 4.7 30.5 1.0
C P:CYS397 4.8 29.1 1.0
C P:GLN328 4.8 26.4 1.0
N P:ALA398 4.9 27.1 1.0
C P:CYS329 4.9 24.8 1.0
CG2 P:ILE396 4.9 28.2 1.0
N P:ILE396 5.0 24.1 1.0
N P:SER399 5.0 22.5 1.0
CA P:ILE396 5.0 26.2 1.0

Zinc binding site 7 out of 16 in 5yj1

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Zinc binding site 7 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn502

b:35.6
occ:1.00
 SG S:CYS394 2.3 24.9 1.0
SG S:CYS326 2.3 26.9 1.0
SG S:CYS329 2.3 24.8 1.0
SG S:CYS397 2.3 25.8 1.0
CB S:CYS394 3.2 24.9 1.0
CB S:CYS326 3.2 25.4 1.0
CB S:CYS329 3.3 27.7 1.0
CB S:CYS397 3.4 26.1 1.0
N S:CYS329 3.7 28.4 1.0
N S:CYS397 3.8 28.4 1.0
CA S:CYS329 4.1 25.9 1.0
CA S:CYS397 4.1 27.9 1.0
CB S:ILE396 4.5 28.0 1.0
CB S:SER399 4.5 25.1 1.0
OG1 S:THR332 4.6 30.0 1.0
CB S:GLN328 4.6 25.5 1.0
CA S:CYS394 4.6 28.0 1.0
CB S:THR332 4.7 27.4 1.0
CA S:CYS326 4.7 22.2 1.0
C S:CYS397 4.8 29.6 1.0
C S:ILE396 4.8 29.7 1.0
C S:GLN328 4.8 28.2 1.0
N S:ALA398 4.9 27.2 1.0
C S:CYS329 4.9 26.8 1.0
CG2 S:ILE396 5.0 27.7 1.0
N S:SER399 5.0 24.3 1.0
N S:ILE396 5.0 24.6 1.0

Zinc binding site 8 out of 16 in 5yj1

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Zinc binding site 8 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn502

b:34.0
occ:1.00
 SG V:CYS394 2.3 22.8 1.0
SG V:CYS397 2.3 22.2 1.0
SG V:CYS326 2.3 22.6 1.0
SG V:CYS329 2.3 23.1 1.0
CB V:CYS326 3.2 18.2 1.0
CB V:CYS394 3.2 21.7 1.0
CB V:CYS329 3.3 23.8 1.0
CB V:CYS397 3.4 24.0 1.0
N V:CYS329 3.7 25.8 1.0
N V:CYS397 3.8 25.1 1.0
CA V:CYS329 4.1 24.6 1.0
CA V:CYS397 4.1 22.6 1.0
CB V:ILE396 4.5 27.5 1.0
CB V:GLN328 4.5 23.9 1.0
OG1 V:THR332 4.6 27.1 1.0
CA V:CYS326 4.6 21.7 1.0
CB V:THR332 4.7 25.7 1.0
CA V:CYS394 4.7 20.2 1.0
OG V:SER399 4.8 32.6 1.0
C V:GLN328 4.8 25.9 1.0
C V:ILE396 4.8 29.2 1.0
CB V:SER399 4.8 27.0 1.0
C V:CYS397 4.9 26.8 1.0
CG2 V:ILE396 4.9 31.9 1.0
C V:CYS326 4.9 23.2 1.0
C V:CYS329 5.0 25.2 1.0

Zinc binding site 9 out of 16 in 5yj1

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Zinc binding site 9 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn502

b:38.6
occ:1.00
 SG Y:CYS394 2.3 27.6 1.0
SG Y:CYS397 2.3 27.9 1.0
SG Y:CYS329 2.3 31.2 1.0
SG Y:CYS326 2.3 27.0 1.0
CB Y:CYS394 3.2 33.4 1.0
CB Y:CYS326 3.3 27.4 1.0
CB Y:CYS329 3.4 31.8 1.0
CB Y:CYS397 3.4 32.3 1.0
N Y:CYS329 3.7 31.9 1.0
N Y:CYS397 3.8 34.5 1.0
CA Y:CYS329 4.1 30.9 1.0
CA Y:CYS397 4.2 30.4 1.0
CB Y:ILE396 4.4 35.4 1.0
CB Y:GLN328 4.5 27.1 1.0
OG1 Y:THR332 4.6 27.9 1.0
CB Y:THR332 4.6 29.9 1.0
CA Y:CYS394 4.7 30.3 1.0
CA Y:CYS326 4.7 26.6 1.0
C Y:GLN328 4.8 32.6 1.0
CG2 Y:ILE396 4.8 38.7 1.0
C Y:ILE396 4.8 34.9 1.0
C Y:CYS397 4.8 32.2 1.0
CB Y:SER399 4.9 34.3 1.0
C Y:CYS329 4.9 30.5 1.0
N Y:GLN328 5.0 30.1 1.0
CA Y:GLN328 5.0 29.5 1.0
C Y:CYS326 5.0 28.4 1.0

Zinc binding site 10 out of 16 in 5yj1

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Zinc binding site 10 out of 16 in the Mouse Cereblon Thalidomide Binding Domain Complexed with R-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 R-Form Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Zn502

b:37.5
occ:1.00
 SG b:CYS394 2.3 24.6 1.0
SG b:CYS329 2.3 24.7 1.0
SG b:CYS326 2.3 25.5 1.0
SG b:CYS397 2.3 26.7 1.0
CB b:CYS394 3.2 25.7 1.0
CB b:CYS326 3.2 22.8 1.0
CB b:CYS329 3.3 25.9 1.0
CB b:CYS397 3.4 25.1 1.0
N b:CYS329 3.8 27.6 1.0
N b:CYS397 3.8 28.6 1.0
CA b:CYS329 4.1 25.3 1.0
CA b:CYS397 4.2 27.6 1.0
CB b:ILE396 4.5 26.1 1.0
CB b:SER399 4.5 26.1 1.0
OG1 b:THR332 4.6 27.4 1.0
CB b:THR332 4.6 25.3 1.0
CA b:CYS394 4.6 25.8 1.0
CB b:GLN328 4.7 23.8 1.0
CA b:CYS326 4.7 21.4 1.0
C b:ILE396 4.8 29.7 1.0
C b:CYS397 4.8 29.6 1.0
C b:GLN328 4.8 27.0 1.0
N b:ALA398 4.9 26.8 1.0
CG2 b:ILE396 4.9 24.9 1.0
C b:CYS329 4.9 26.3 1.0
N b:SER399 5.0 23.9 1.0
N b:ILE396 5.0 23.6 1.0
CA b:ILE396 5.0 25.5 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 15:48:20 2024

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