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Zinc in PDB 3wx1: Mouse Cereblon Thalidomide Binding Domain, Selenomethionine Derivative

Protein crystallography data

The structure of Mouse Cereblon Thalidomide Binding Domain, Selenomethionine Derivative, PDB code: 3wx1 was solved by T.Mori, T.Ito, Y.Hirano, Y.Yamaguchi, H.Handa, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.10 / 1.93
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 118.112, 118.112, 118.112, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Mouse Cereblon Thalidomide Binding Domain, Selenomethionine Derivative (pdb code 3wx1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mouse Cereblon Thalidomide Binding Domain, Selenomethionine Derivative, PDB code: 3wx1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wx1

Go back to Zinc Binding Sites List in 3wx1
Zinc binding site 1 out of 2 in the Mouse Cereblon Thalidomide Binding Domain, Selenomethionine Derivative


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, Selenomethionine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:33.1
occ:1.00
SG A:CYS326 2.3 33.3 1.0
SG A:CYS329 2.3 34.4 1.0
SG A:CYS397 2.3 35.0 1.0
SG A:CYS394 2.3 30.1 1.0
CB A:CYS326 3.1 33.2 1.0
CB A:CYS394 3.2 31.1 1.0
CB A:CYS329 3.3 35.1 1.0
CB A:CYS397 3.4 33.0 1.0
N A:CYS329 3.7 35.7 1.0
N A:CYS397 3.9 33.7 1.0
CA A:CYS329 4.1 33.2 1.0
CA A:CYS397 4.2 35.9 1.0
CB A:ILE396 4.4 32.6 1.0
OG1 A:THR332 4.5 32.2 1.0
CB A:THR332 4.6 30.6 1.0
CA A:CYS326 4.6 34.7 1.0
CB A:GLN328 4.6 35.4 1.0
CA A:CYS394 4.6 31.6 1.0
OG A:SER399 4.7 44.7 1.0
CG2 A:ILE396 4.8 34.9 1.0
C A:GLN328 4.8 38.1 1.0
C A:ILE396 4.8 33.8 1.0
C A:CYS397 4.9 35.4 1.0
CB A:SER399 5.0 41.5 1.0
CA A:ILE396 5.0 34.9 1.0
N A:ALA398 5.0 36.7 1.0

Zinc binding site 2 out of 2 in 3wx1

Go back to Zinc Binding Sites List in 3wx1
Zinc binding site 2 out of 2 in the Mouse Cereblon Thalidomide Binding Domain, Selenomethionine Derivative


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, Selenomethionine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:40.0
occ:1.00
SG B:CYS326 2.3 39.6 1.0
SG B:CYS329 2.3 45.0 1.0
SG B:CYS397 2.3 41.7 1.0
SG B:CYS394 2.4 33.9 1.0
CB B:CYS326 3.2 38.2 1.0
CB B:CYS394 3.2 35.2 1.0
CB B:CYS329 3.3 47.8 1.0
CB B:CYS397 3.4 42.9 1.0
N B:CYS329 3.8 48.7 1.0
N B:CYS397 3.9 40.6 1.0
CA B:CYS329 4.1 46.0 1.0
CA B:CYS397 4.2 40.0 1.0
OG1 B:THR332 4.4 44.2 1.0
CB B:ILE396 4.4 43.4 1.0
CB B:THR332 4.6 43.9 1.0
CA B:CYS326 4.7 37.1 1.0
CB B:SER399 4.7 36.3 1.0
CA B:CYS394 4.7 32.8 1.0
CB B:GLN328 4.8 54.0 1.0
C B:CYS397 4.8 42.6 1.0
C B:GLN328 4.9 53.2 1.0
C B:ILE396 4.9 43.2 1.0
N B:ALA398 4.9 38.6 1.0
CG2 B:ILE396 4.9 43.5 1.0
N B:ILE396 5.0 40.0 1.0
C B:CYS329 5.0 45.8 1.0

Reference:

P.P.Chamberlain, A.Lopez-Girona, K.Miller, G.Carmel, B.Pagarigan, B.Chie-Leon, E.Rychak, L.G.Corral, Y.J.Ren, M.Wang, M.Riley, S.L.Delker, T.Ito, H.Ando, T.Mori, Y.Hirano, H.Handa, T.Hakoshima, T.O.Daniel, B.E.Cathers. Structure of the Human Cereblon-DDB1-Lenalidomide Complex Reveals Basis For Responsiveness to Thalidomide Analogs Nat.Struct.Mol.Biol. V. 21 803 2014.
ISSN: ISSN 1545-9993
PubMed: 25108355
DOI: 10.1038/NSMB.2874
Page generated: Wed Dec 16 04:58:10 2020

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