Zinc in PDB 8u16: The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide

The structure of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide, PDB code: 8u16 was solved by M.C.Clifton, X.Ma, E.Ornelas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.35 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.536, 151.986, 218.46, 90, 90, 90
R / Rfree (%)	21.9 / 27.3

The binding sites of Zinc atom in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide (pdb code 8u16). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide, PDB code: 8u16:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:69.1 occ:1.00 SG A:CYS394 2.2 68.4 1.0 SG A:CYS326 2.2 81.5 1.0 SG A:CYS323 2.4 83.4 1.0 SG A:CYS391 2.5 64.5 1.0 CB A:CYS391 3.1 71.4 1.0 CB A:CYS323 3.3 70.5 1.0 CB A:CYS394 3.4 74.9 1.0 CB A:CYS326 3.5 79.1 1.0 N A:CYS394 3.7 68.2 1.0 N A:CYS326 3.8 76.7 1.0 CA A:CYS394 4.1 66.6 1.0 OG1 A:THR329 4.2 100.5 1.0 CA A:CYS326 4.3 76.4 1.0 CB A:GLN325 4.4 74.2 1.0 OG A:SER396 4.5 72.3 1.0 CA A:CYS391 4.6 71.5 1.0 CB A:ILE393 4.6 67.9 1.0 CB A:SER396 4.7 65.6 1.0 C A:CYS394 4.7 61.4 1.0 CA A:CYS323 4.7 71.5 1.0 CB A:THR329 4.7 98.2 1.0 C A:ILE393 4.8 65.2 1.0 N A:ALA395 4.8 63.5 1.0 N A:SER396 4.8 68.3 1.0 C A:GLN325 4.9 76.6 1.0 N A:ILE393 5.0 70.7 1.0

Zinc binding site 2 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:87.0 occ:1.00 NE2 C:HIS404 2.0 92.4 1.0 SG C:CYS387 2.3 77.4 1.0 NE2 C:HIS400 2.4 90.9 1.0 SG C:CYS384 2.5 93.4 1.0 CD2 C:HIS404 2.8 97.3 1.0 CD2 C:HIS400 3.1 90.4 1.0 CE1 C:HIS404 3.1 96.8 1.0 CB C:CYS384 3.2 85.1 1.0 CB C:CYS387 3.6 83.5 1.0 CE1 C:HIS400 3.6 92.8 1.0 N C:CYS387 3.8 85.7 1.0 CG C:HIS404 4.0 101.2 1.0 ND1 C:HIS404 4.1 102.1 1.0 CA C:CYS387 4.2 81.1 1.0 CG C:HIS400 4.4 95.0 1.0 ND1 C:HIS400 4.6 95.6 1.0 CA C:CYS384 4.6 83.5 1.0 CB C:TYR386 4.7 93.0 1.0 CB C:LYS389 4.8 77.3 1.0 C C:CYS387 4.8 81.0 1.0 N C:SER388 4.8 78.7 1.0 N C:LYS389 4.8 79.5 1.0 C C:TYR386 4.9 87.1 1.0 N C:TYR386 5.0 90.2 1.0 C C:CYS384 5.0 86.1 1.0

Zinc binding site 3 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:86.0 occ:1.00 SG C:CYS415 1.9 55.1 1.0 NE2 C:HIS432 2.0 71.9 1.0 SG C:CYS412 2.3 55.7 1.0 NE2 C:HIS428 2.3 82.8 1.0 CD2 C:HIS432 2.7 72.0 1.0 CD2 C:HIS428 2.9 80.9 1.0 CE1 C:HIS432 3.0 73.0 1.0 CE1 C:HIS428 3.4 83.2 1.0 CB C:CYS415 3.5 65.5 1.0 CB C:CYS412 3.5 69.0 1.0 N C:CYS415 3.8 70.4 1.0 CG C:HIS432 3.9 73.5 1.0 ND1 C:HIS432 4.0 74.0 1.0 CG C:HIS428 4.1 78.6 1.0 CA C:CYS415 4.2 69.0 1.0 CB C:VAL414 4.3 61.9 1.0 ND1 C:HIS428 4.3 82.2 1.0 CG1 C:VAL414 4.7 57.5 1.0 O C:HIS428 4.7 82.2 1.0 C C:VAL414 4.7 65.4 1.0 CB C:HIS417 4.8 71.5 1.0 CA C:CYS412 4.9 63.5 1.0 CA C:VAL414 4.9 66.4 1.0

Zinc binding site 4 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:57.0 occ:1.00 SG D:CYS394 2.3 62.6 1.0 SG D:CYS391 2.4 53.0 1.0 SG D:CYS323 2.4 75.3 1.0 SG D:CYS326 2.5 74.1 1.0 CB D:CYS326 3.1 77.5 1.0 CB D:CYS394 3.2 62.5 1.0 CB D:CYS323 3.3 68.8 1.0 N D:CYS326 3.4 74.9 1.0 CB D:CYS391 3.4 61.7 1.0 N D:CYS394 3.7 64.2 1.0 CA D:CYS326 3.9 76.3 1.0 CA D:CYS394 4.0 63.1 1.0 OG1 D:THR329 4.1 76.1 1.0 CB D:GLN325 4.3 77.0 1.0 C D:GLN325 4.5 80.0 1.0 CB D:ILE393 4.6 64.7 1.0 CA D:CYS323 4.7 68.0 1.0 CA D:GLN325 4.8 76.7 1.0 OG D:SER396 4.8 62.7 1.0 C D:CYS394 4.8 66.3 1.0 C D:ILE393 4.8 66.9 1.0 CA D:CYS391 4.9 62.6 1.0 N D:GLN325 4.9 76.4 1.0 C D:CYS326 4.9 81.7 1.0

Zinc binding site 5 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:79.5 occ:1.00 NE2 F:HIS404 2.1 87.7 1.0 NE2 F:HIS400 2.3 86.7 1.0 SG F:CYS384 2.4 79.7 1.0 SG F:CYS387 2.4 87.7 1.0 CD2 F:HIS400 2.9 91.5 1.0 CD2 F:HIS404 2.9 92.1 1.0 CE1 F:HIS404 3.2 89.7 1.0 CB F:CYS384 3.3 82.9 1.0 CE1 F:HIS400 3.5 88.9 1.0 CB F:CYS387 3.7 83.5 1.0 N F:CYS387 3.9 79.6 1.0 CG F:HIS404 4.1 92.1 1.0 CG F:HIS400 4.2 97.5 1.0 ND1 F:HIS404 4.2 92.3 1.0 CA F:CYS387 4.4 79.4 1.0 ND1 F:HIS400 4.4 100.1 1.0 CB F:TYR386 4.7 82.7 1.0 CA F:CYS384 4.7 84.5 1.0 CB F:LYS389 4.9 73.3 1.0 N F:SER388 4.9 80.3 1.0 N F:LYS389 4.9 76.5 1.0 C F:CYS387 4.9 79.0 1.0 C F:TYR386 5.0 80.3 1.0

Zinc binding site 6 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:56.3 occ:1.00 NE2 F:HIS432 2.0 60.9 1.0 SG F:CYS415 2.1 55.8 1.0 SG F:CYS412 2.2 52.1 1.0 NE2 F:HIS428 2.3 62.6 1.0 CE1 F:HIS432 2.9 57.5 1.0 CD2 F:HIS428 3.0 61.2 1.0 CD2 F:HIS432 3.1 61.3 1.0 CB F:CYS412 3.3 56.1 1.0 N F:CYS415 3.3 54.9 1.0 CE1 F:HIS428 3.3 64.8 1.0 CB F:CYS415 3.5 52.7 1.0 CA F:CYS415 3.9 54.2 1.0 ND1 F:HIS432 4.1 60.9 1.0 CB F:VAL414 4.2 55.6 1.0 CG F:HIS432 4.2 58.6 1.0 CG F:HIS428 4.3 61.0 1.0 C F:VAL414 4.3 53.6 1.0 ND1 F:HIS428 4.4 65.9 1.0 CB F:HIS417 4.4 60.0 1.0 CG1 F:VAL414 4.5 51.9 1.0 CA F:VAL414 4.6 56.1 1.0 N F:VAL414 4.7 58.2 1.0 CA F:CYS412 4.7 57.6 1.0 O F:HIS428 4.9 68.0 1.0 N F:GLY416 4.9 53.6 1.0 N F:HIS417 4.9 55.0 1.0 C F:CYS415 5.0 54.9 1.0

X.Ma, B.Leon, E.Ornelas, D.Dovala, L.Tandeske, C.Luu, G.Pardee, S.Widger, J.M.Solomon, R.E.J.Beckwith, H.Moser, M.C.Clifton, C.A.Wartchow. Structural and Biophysical Comparisons of the Pomalidomide- and Cc-220-Induced Interactions of SALL4 with Cereblon. Sci Rep V. 13 22088 2023.
ISSN: ESSN 2045-2322
PubMed: 38086859
DOI: 10.1038/S41598-023-48606-3