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Zinc in PDB 4tzc: Crystal Structure of Murine Cereblon in Complex with Thalidomide

Protein crystallography data

The structure of Crystal Structure of Murine Cereblon in Complex with Thalidomide, PDB code: 4tzc was solved by P.P.Chamberlain, B.Pagarigan, S.Delker, B.Leon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.88
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 143.146, 143.146, 143.146, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Murine Cereblon in Complex with Thalidomide (pdb code 4tzc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Murine Cereblon in Complex with Thalidomide, PDB code: 4tzc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4tzc

Go back to Zinc Binding Sites List in 4tzc
Zinc binding site 1 out of 4 in the Crystal Structure of Murine Cereblon in Complex with Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Murine Cereblon in Complex with Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:20.7
occ:1.00
SG C:CYS325 2.3 18.9 1.0
SG C:CYS328 2.3 21.1 1.0
SG C:CYS396 2.4 20.2 1.0
SG C:CYS393 2.4 19.3 1.0
CB C:CYS325 3.1 18.9 1.0
CB C:CYS393 3.1 18.7 1.0
CB C:CYS328 3.2 19.1 1.0
CB C:CYS396 3.4 20.3 1.0
N C:CYS328 3.7 18.9 1.0
N C:CYS396 3.8 19.3 1.0
CA C:CYS328 4.0 18.8 1.0
CA C:CYS396 4.2 20.7 1.0
OG1 C:THR331 4.5 21.2 1.0
CB C:THR331 4.6 20.2 1.0
CB C:ILE395 4.6 22.2 1.0
CA C:CYS325 4.6 18.7 1.0
CB C:SER398 4.6 21.6 1.0
CA C:CYS393 4.6 18.7 1.0
CB C:GLN327 4.7 20.1 1.0
C C:ILE395 4.7 20.6 1.0
C C:CYS396 4.8 21.8 1.0
C C:GLN327 4.8 19.9 1.0
C C:CYS328 4.9 18.1 1.0
N C:SER398 5.0 19.0 1.0
N C:ALA397 5.0 19.5 1.0
N C:ILE395 5.0 19.2 1.0

Zinc binding site 2 out of 4 in 4tzc

Go back to Zinc Binding Sites List in 4tzc
Zinc binding site 2 out of 4 in the Crystal Structure of Murine Cereblon in Complex with Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Murine Cereblon in Complex with Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:18.3
occ:1.00
SG A:CYS328 2.3 18.4 1.0
SG A:CYS396 2.3 17.2 1.0
SG A:CYS393 2.3 16.4 1.0
SG A:CYS325 2.4 17.5 1.0
CB A:CYS393 3.1 15.1 1.0
CB A:CYS325 3.1 15.9 1.0
CB A:CYS328 3.3 18.0 1.0
CB A:CYS396 3.4 19.2 1.0
N A:CYS328 3.7 18.3 1.0
N A:CYS396 3.8 16.7 1.0
CA A:CYS328 4.1 19.7 1.0
CA A:CYS396 4.2 16.1 1.0
CB A:ILE395 4.5 19.4 1.0
OG1 A:THR331 4.5 22.2 1.0
CA A:CYS393 4.6 15.5 1.0
CA A:CYS325 4.6 17.2 1.0
CB A:THR331 4.6 20.5 1.0
CB A:GLN327 4.7 18.9 1.0
OG A:SER398 4.8 26.8 1.0
C A:ILE395 4.8 21.5 1.0
C A:GLN327 4.9 22.1 1.0
CB A:SER398 4.9 20.1 1.0
C A:CYS396 4.9 19.8 1.0
C A:CYS328 5.0 20.4 1.0

Zinc binding site 3 out of 4 in 4tzc

Go back to Zinc Binding Sites List in 4tzc
Zinc binding site 3 out of 4 in the Crystal Structure of Murine Cereblon in Complex with Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Murine Cereblon in Complex with Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:28.1
occ:1.00
SG B:CYS328 2.2 27.8 1.0
SG B:CYS325 2.4 24.3 1.0
SG B:CYS393 2.4 25.6 1.0
SG B:CYS396 2.4 26.4 1.0
CB B:CYS393 3.2 23.2 1.0
CB B:CYS325 3.2 25.7 1.0
CB B:CYS328 3.3 31.7 1.0
CB B:CYS396 3.4 31.3 1.0
N B:CYS328 3.8 27.5 1.0
N B:CYS396 3.8 31.4 1.0
OG1 B:THR331 4.0 28.5 1.0
CA B:CYS328 4.1 28.8 1.0
CA B:CYS396 4.2 27.4 1.0
CB B:ILE395 4.6 29.3 1.0
CA B:CYS325 4.6 24.3 1.0
CB B:SER398 4.7 28.4 1.0
CA B:CYS393 4.7 25.5 1.0
CB B:GLN327 4.7 31.4 1.0
C B:CYS328 4.8 31.7 1.0
N B:GLN329 4.8 29.3 1.0
C B:GLN327 4.8 32.9 1.0
C B:CYS396 4.8 32.9 1.0
C B:ILE395 4.9 33.5 1.0
N B:ALA397 5.0 29.6 1.0

Zinc binding site 4 out of 4 in 4tzc

Go back to Zinc Binding Sites List in 4tzc
Zinc binding site 4 out of 4 in the Crystal Structure of Murine Cereblon in Complex with Thalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Murine Cereblon in Complex with Thalidomide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:26.2
occ:1.00
SG D:CYS328 2.3 27.9 1.0
SG D:CYS393 2.3 23.6 1.0
SG D:CYS396 2.3 25.9 1.0
SG D:CYS325 2.4 24.0 1.0
CB D:CYS393 3.1 21.5 1.0
CB D:CYS325 3.2 20.7 1.0
CB D:CYS328 3.3 33.4 1.0
CB D:CYS396 3.3 26.5 1.0
N D:CYS328 3.7 27.4 1.0
N D:CYS396 3.8 23.0 1.0
CA D:CYS328 4.1 30.1 1.0
CA D:CYS396 4.1 26.4 1.0
CB D:ILE395 4.4 30.9 1.0
CA D:CYS393 4.6 23.7 1.0
OG1 D:THR331 4.6 31.0 1.0
CA D:CYS325 4.7 24.3 1.0
CB D:THR331 4.7 30.0 1.0
CB D:SER398 4.7 26.4 1.0
CB D:GLN327 4.7 25.8 1.0
C D:ILE395 4.8 30.0 1.0
CG2 D:ILE395 4.8 29.1 1.0
C D:GLN327 4.8 32.1 1.0
C D:CYS396 4.8 25.6 1.0
CA D:ILE395 5.0 28.8 1.0
C D:CYS328 5.0 28.0 1.0
CG D:GLN327 5.0 34.4 1.0

Reference:

P.P.Chamberlain, A.Lopez-Girona, K.Miller, G.Carmel, B.Pagarigan, B.Leon, E.Rychak, L.Corral, Y.Ren, M.Wang, M.Riley, S.Delker, T.Ito, A.Hideki, T.Mori, Y.Hirano, H.Handa, T.Hakoshima, T.O.Daniel, B.E.Cathers. Structural Basis For Responsiveness to Thalidomide-Analog Drugs Defined By the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex To Be Published.
Page generated: Wed Dec 16 05:47:34 2020

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