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Zinc in PDB 6boy: Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET6 Protac.

Protein crystallography data

The structure of Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET6 Protac., PDB code: 6boy was solved by R.P.Nowak, S.L.Deangelo, D.Buckley, J.E.Bradner, E.S.Fischer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.79 / 3.33
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.406, 115.406, 588.143, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.4

Other elements in 6boy:

The structure of Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET6 Protac. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET6 Protac. (pdb code 6boy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET6 Protac., PDB code: 6boy:

Zinc binding site 1 out of 1 in 6boy

Go back to Zinc Binding Sites List in 6boy
Zinc binding site 1 out of 1 in the Crystal Structure of DDB1-Crbn-BRD4(BD1) Complex Bound to DBET6 Protac.


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 DDB1-Crbn-BRD4(BD1) Complex Bound to DBET6 Protac. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:0.8
occ:1.00
SG B:CYS394 2.3 0.2 1.0
SG B:CYS323 2.3 0.5 1.0
SG B:CYS326 2.3 0.8 1.0
SG B:CYS391 2.4 0.2 1.0
CB B:CYS391 3.0 0.8 1.0
CB B:CYS323 3.0 0.8 1.0
CB B:CYS326 3.2 0.6 1.0
CB B:CYS394 3.5 0.9 1.0
N B:CYS326 3.7 0.2 1.0
N B:CYS394 4.0 93.8 1.0
CA B:CYS326 4.0 0.2 1.0
CA B:CYS394 4.3 0.1 1.0
CA B:CYS391 4.5 92.7 1.0
CA B:CYS323 4.5 0.8 1.0
CB B:GLN325 4.7 98.3 1.0
CB B:THR329 4.7 0.3 1.0
C B:GLN325 4.7 0.5 1.0
OG1 B:THR329 4.7 0.4 1.0
CB B:SER396 4.8 0.5 1.0
C B:CYS394 4.9 0.2 1.0
OG B:SER396 4.9 0.1 1.0
N B:SER396 5.0 0.6 1.0

Reference:

R.P.Nowak, S.L.Deangelo, D.Buckley, Z.He, K.A.Donovan, J.An, N.Safaee, M.P.Jedrychowski, C.M.Ponthier, M.Ishoey, T.Zhang, J.D.Mancias, N.S.Gray, J.E.Bradner, E.S.Fischer. Plasticity in Binding Confers Selectivity in Ligand-Induced Protein Degradation. Nat. Chem. Biol. V. 14 706 2018.
ISSN: ESSN 1552-4469
PubMed: 29892083
DOI: 10.1038/S41589-018-0055-Y
Page generated: Wed Dec 16 11:32:55 2020

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