Zinc in PDB 6h0g: Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4)

The structure of Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4), PDB code: 6h0g was solved by R.D.Bunker, G.Petzold, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 4.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	112.510, 99.530, 166.940, 90.00, 108.49, 90.00
R / Rfree (%)	22.1 / 25.6

The binding sites of Zinc atom in the Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4) (pdb code 6h0g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4), PDB code: 6h0g:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:75.0 occ:1.00 SG B:CYS326 2.3 0.2 1.0 SG B:CYS391 2.5 0.4 1.0 SG B:CYS323 2.6 1.0 1.0 SG B:CYS394 2.7 0.5 1.0 HB2 B:CYS326 2.8 0.7 0.0 HB3 B:CYS323 3.1 0.2 0.0 HB2 B:CYS323 3.1 0.1 0.0 CB B:CYS323 3.1 0.2 1.0 HB2 B:CYS391 3.2 0.9 0.0 CB B:CYS326 3.2 0.6 1.0 HB3 B:CYS391 3.2 1.0 0.0 CB B:CYS391 3.2 0.2 1.0 H B:CYS326 3.2 0.7 0.0 H B:CYS394 3.3 0.1 0.0 HG1 B:THR329 3.4 0.7 0.0 HB B:THR329 3.5 0.3 0.0 HB3 B:CYS394 3.8 0.0 0.0 HB B:ILE393 3.8 0.1 0.0 HB3 B:GLN325 3.9 0.2 0.0 N B:CYS326 3.9 0.3 1.0 CB B:CYS394 3.9 0.7 1.0 HB3 B:CYS326 4.0 0.6 0.0 HD11 B:ILE398 4.1 0.8 0.0 CA B:CYS326 4.1 0.3 1.0 OG1 B:THR329 4.1 0.2 1.0 HB2 B:SER396 4.1 0.0 0.0 HG21 B:THR329 4.2 0.0 0.0 N B:CYS394 4.3 0.7 1.0 CB B:THR329 4.3 0.2 1.0 H B:ILE393 4.5 0.0 0.0 H B:SER396 4.5 0.1 0.0 HA B:CYS326 4.6 0.6 0.0 CA B:CYS323 4.6 0.2 1.0 CA B:CYS394 4.7 0.4 1.0 CA B:CYS391 4.7 0.5 1.0 H B:GLN325 4.7 0.9 0.0 CG2 B:THR329 4.7 0.7 1.0 HB2 B:CYS394 4.8 0.0 0.0 HD11 B:ILE331 4.8 0.5 0.0 CB B:ILE393 4.9 0.9 1.0 CB B:GLN325 4.9 0.6 1.0 HD13 B:ILE393 4.9 0.9 0.0 C B:GLN325 5.0 0.4 1.0 HG22 B:ILE393 5.0 0.2 0.0

Zinc binding site 2 out of 4 in the Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:75.0 occ:1.00 NE2 C:HIS435 2.0 90.1 1.0 SG C:CYS419 2.2 78.4 1.0 SG C:CYS422 2.5 82.4 1.0 HD2 C:HIS435 2.5 83.9 0.0 CD2 C:HIS435 2.5 85.4 1.0 NE2 C:HIS439 2.6 0.8 1.0 HD2 C:HIS439 2.7 94.7 0.0 HB3 C:CYS419 2.8 76.9 0.0 CD2 C:HIS439 3.0 99.8 1.0 CB C:CYS419 3.0 76.4 1.0 HB C:ILE421 3.0 83.9 0.0 HB3 C:PHE424 3.0 79.9 0.0 HB2 C:CYS419 3.2 76.5 0.0 H C:CYS422 3.2 80.1 0.0 CE1 C:HIS435 3.2 92.9 1.0 HE1 C:HIS435 3.8 98.5 0.0 CG C:HIS435 3.8 85.4 1.0 HD12 C:ILE421 3.8 86.8 0.0 H C:PHE424 3.8 80.4 0.0 CE1 C:HIS439 3.9 0.1 1.0 H C:ILE421 3.9 80.8 0.0 N C:CYS422 3.9 82.0 1.0 CB C:CYS422 4.0 85.1 1.0 HD2 C:PHE424 4.0 79.1 0.0 CB C:PHE424 4.0 82.5 1.0 HA C:GLN436 4.1 88.7 0.0 CB C:ILE421 4.1 86.5 1.0 HG2 C:GLN436 4.1 88.1 0.0 ND1 C:HIS435 4.1 90.2 1.0 HB2 C:PHE424 4.1 84.8 0.0 HB3 C:CYS422 4.3 86.9 0.0 HG3 C:GLN436 4.3 83.0 0.0 CG C:HIS439 4.3 0.5 1.0 HE1 C:HIS439 4.4 0.5 0.0 CA C:CYS419 4.4 76.0 1.0 HG22 C:ILE421 4.5 89.3 0.0 CA C:CYS422 4.5 83.7 1.0 HB2 B:HIS397 4.6 0.6 0.0 CD2 C:PHE424 4.6 81.5 1.0 N C:ILE421 4.6 82.2 1.0 CD1 C:ILE421 4.7 90.5 1.0 CA C:ILE421 4.7 85.0 1.0 CG C:GLN436 4.7 85.7 1.0 CG C:PHE424 4.7 83.7 1.0 C C:ILE421 4.7 84.5 1.0 H C:GLY423 4.7 79.3 0.0 ND1 C:HIS439 4.7 0.8 1.0 N C:PHE424 4.7 81.6 1.0 CG2 C:ILE421 4.8 90.6 1.0 HB2 C:CYS422 4.8 87.5 0.0 HD13 C:ILE421 4.8 92.9 0.0 C C:CYS419 4.9 76.8 1.0 CG1 C:ILE421 4.9 89.5 1.0 HA C:CYS419 4.9 76.5 0.0 CA C:GLN436 5.0 87.5 1.0

Zinc binding site 3 out of 4 in the Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:75.0 occ:1.00 SG E:CYS391 2.2 0.9 1.0 SG E:CYS326 2.7 0.9 1.0 SG E:CYS394 2.8 0.4 1.0 CB E:CYS391 2.8 0.2 1.0 HB2 E:CYS391 2.8 0.8 0.0 SG E:CYS323 2.8 0.2 1.0 HB3 E:CYS391 2.8 0.4 0.0 HB2 E:CYS323 3.1 0.3 0.0 H E:CYS394 3.2 0.6 0.0 HB2 E:CYS326 3.2 0.7 0.0 HB3 E:CYS323 3.3 0.6 0.0 CB E:CYS323 3.3 0.2 1.0 HG1 E:THR329 3.4 0.5 0.0 CB E:CYS326 3.6 0.1 1.0 HB E:THR329 3.6 0.1 0.0 H E:CYS326 3.6 0.3 0.0 HB E:ILE393 3.7 0.9 0.0 HD11 E:ILE398 3.9 0.3 0.0 HB3 E:CYS394 3.9 0.1 0.0 HG21 E:THR329 4.0 1.0 0.0 CB E:CYS394 4.0 0.8 1.0 HB2 E:SER396 4.1 0.8 0.0 N E:CYS394 4.1 0.2 1.0 H E:ILE393 4.1 0.1 0.0 HB3 E:GLN325 4.2 0.2 0.0 OG1 E:THR329 4.2 0.0 1.0 CA E:CYS391 4.3 0.1 1.0 CB E:THR329 4.3 0.9 1.0 HB3 E:CYS326 4.3 0.2 0.0 H E:SER396 4.3 0.6 0.0 N E:CYS326 4.3 1.0 1.0 CA E:CYS326 4.6 0.6 1.0 HD11 E:ILE331 4.6 0.6 0.0 CG2 E:THR329 4.6 0.5 1.0 CA E:CYS394 4.6 0.7 1.0 HA E:CYS391 4.6 0.5 0.0 CB E:ILE393 4.8 0.8 1.0 H E:ALA395 4.8 0.6 0.0 HD13 E:ILE393 4.8 0.8 0.0 CA E:CYS323 4.8 0.7 1.0 HD12 E:ILE393 4.9 0.9 0.0 HB2 E:CYS394 4.9 0.1 0.0 C E:CYS391 4.9 0.9 1.0 HG22 E:THR329 4.9 0.8 0.0 H E:CYS391 4.9 0.3 0.0 H E:GLN325 5.0 0.1 0.0

Zinc binding site 4 out of 4 in the Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the DDB1-Crbn-Pomalidomide Complex Bound to ZNF692(ZF4) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:75.0 occ:1.00 NE2 F:HIS439 2.0 0.9 1.0 SG F:CYS422 2.3 0.7 1.0 SG F:CYS419 2.7 0.8 1.0 NE2 F:HIS435 2.7 0.6 1.0 HB F:ILE421 2.8 0.2 0.0 CD2 F:HIS439 2.9 0.9 1.0 CE1 F:HIS439 2.9 0.7 1.0 HB3 F:CYS419 3.0 0.7 0.0 HD2 F:HIS435 3.0 0.1 0.0 H F:CYS422 3.0 0.1 0.0 HD2 F:HIS439 3.1 0.6 0.0 CD2 F:HIS435 3.2 0.3 1.0 HE1 F:HIS439 3.2 0.9 0.0 HB3 F:PHE424 3.2 0.7 0.0 CB F:CYS419 3.3 0.2 1.0 HB2 F:CYS419 3.6 0.6 0.0 CB F:CYS422 3.7 0.8 1.0 N F:CYS422 3.7 0.7 1.0 HB3 F:CYS422 3.8 0.7 0.0 CB F:ILE421 3.8 0.6 1.0 HD12 F:ILE421 3.8 0.1 0.0 H F:ILE421 3.9 0.4 0.0 H F:PHE424 3.9 1.0 0.0 CE1 F:HIS435 3.9 0.9 1.0 CG F:HIS439 3.9 0.9 1.0 ND1 F:HIS439 3.9 0.8 1.0 HG22 F:ILE421 4.1 0.1 0.0 HB2 F:PHE424 4.1 0.8 0.0 CB F:PHE424 4.1 0.1 1.0 CA F:CYS422 4.2 0.2 1.0 HB2 E:HIS397 4.3 0.1 0.0 HE1 F:HIS435 4.4 0.6 0.0 CG F:HIS435 4.4 0.1 1.0 C F:ILE421 4.4 0.0 1.0 HD2 F:PHE424 4.4 0.1 0.0 CG2 F:ILE421 4.4 0.2 1.0 CA F:ILE421 4.5 0.8 1.0 HB2 F:CYS422 4.5 0.7 0.0 N F:ILE421 4.5 1.0 1.0 CD1 F:ILE421 4.6 0.9 1.0 HG21 F:ILE421 4.7 0.1 0.0 H F:GLY423 4.7 0.3 0.0 HA F:GLN436 4.7 0.3 0.0 CG1 F:ILE421 4.7 0.1 1.0 HD13 F:ILE421 4.7 0.7 0.0 CA F:CYS419 4.7 0.2 1.0 ND1 F:HIS435 4.8 0.5 1.0 HG2 F:GLN436 4.8 0.6 0.0 HB3 E:HIS397 4.8 0.9 0.0 N F:PHE424 4.8 0.1 1.0 HD1 F:HIS439 4.8 0.6 0.0 C F:CYS422 4.9 0.2 1.0 CG F:PHE424 4.9 0.5 1.0 CB E:HIS397 5.0 0.6 1.0 N F:GLY423 5.0 0.6 1.0

Q.L.Sievers, G.Petzold, R.D.Bunker, A.Renneville, M.Slabicki, B.J.Liddicoat, W.Abdulrahman, T.Mikkelsen, B.L.Ebert, N.H.Thoma. Defining the Human C2H2 Zinc Finger Degrome Targeted By Thalidomide Analogs Through Crbn. Science V. 362 2018.
ISSN: ESSN 1095-9203
PubMed: 30385546
DOI: 10.1126/SCIENCE.AAT0572