Zinc in PDB 8u15: The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220

The structure of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220, PDB code: 8u15 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)	61.48 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	110.729, 95.727, 150.947, 90, 91.72, 90
R / Rfree (%)	22 / 27.2

The binding sites of Zinc atom in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220 (pdb code 8u15). 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 Cc-220, PDB code: 8u15:
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 Cc-220


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 Cc-220 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:56.6 occ:1.00 SG A:CYS394 2.3 61.5 1.0 SG A:CYS326 2.3 75.3 1.0 SG A:CYS391 2.3 57.8 1.0 SG A:CYS323 2.6 74.3 1.0 CB A:CYS394 3.1 62.9 1.0 CB A:CYS391 3.1 44.2 1.0 CB A:CYS323 3.2 62.6 1.0 N A:CYS394 3.6 62.9 1.0 CB A:CYS326 3.7 71.8 1.0 CA A:CYS394 3.9 63.3 1.0 N A:CYS326 4.0 68.1 1.0 OG1 A:THR329 4.2 70.0 1.0 CB A:THR329 4.4 66.4 1.0 CA A:CYS326 4.5 70.4 1.0 CB A:GLN325 4.5 64.2 1.0 CA A:CYS391 4.6 50.7 1.0 C A:CYS394 4.6 64.9 1.0 CA A:CYS323 4.7 68.4 1.0 C A:ILE393 4.7 56.2 1.0 CB A:ILE393 4.8 56.3 1.0 N A:ALA395 4.8 61.9 1.0 OG A:SER396 4.8 57.8 1.0 CG2 A:ILE393 4.9 55.3 1.0 N A:ILE393 4.9 53.6 1.0

Zinc binding site 2 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220


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 Cc-220 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:59.5 occ:1.00 NE2 C:HIS404 2.1 77.5 1.0 NE2 C:HIS400 2.1 92.3 1.0 SG C:CYS384 2.2 67.9 1.0 SG C:CYS387 2.3 74.9 1.0 CE1 C:HIS404 3.0 84.3 1.0 CE1 C:HIS400 3.0 85.4 1.0 CD2 C:HIS404 3.2 84.7 1.0 CB C:CYS384 3.2 59.6 1.0 CD2 C:HIS400 3.2 84.2 1.0 CB C:CYS387 3.3 60.9 1.0 N C:CYS387 3.7 64.5 1.0 CA C:CYS387 4.1 59.7 1.0 ND1 C:HIS404 4.2 80.8 1.0 ND1 C:HIS400 4.2 98.9 1.0 CG C:HIS404 4.3 87.7 1.0 CG C:HIS400 4.3 92.6 1.0 CB C:TYR386 4.6 63.1 1.0 CA C:CYS384 4.6 63.5 1.0 C C:TYR386 4.8 63.0 1.0 C C:CYS387 4.8 69.4 1.0 N C:SER388 4.9 69.1 1.0 CB C:LYS389 4.9 61.6 1.0 N C:TYR386 4.9 65.0 1.0 CA C:TYR386 5.0 62.4 1.0 C C:CYS384 5.0 73.9 1.0

Zinc binding site 3 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220


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 Cc-220 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:53.7 occ:1.00 NE2 C:HIS428 2.1 62.7 1.0 NE2 C:HIS432 2.1 62.3 1.0 SG C:CYS415 2.3 76.3 1.0 SG C:CYS412 2.3 46.2 1.0 CD2 C:HIS428 2.7 57.5 1.0 CE1 C:HIS432 2.8 63.9 1.0 CE1 C:HIS428 3.2 72.6 1.0 CB C:CYS412 3.3 54.3 1.0 CD2 C:HIS432 3.4 62.7 1.0 CB C:CYS415 3.6 50.1 1.0 N C:CYS415 3.9 52.1 1.0 CG C:HIS428 3.9 57.1 1.0 ND1 C:HIS432 4.0 65.3 1.0 ND1 C:HIS428 4.2 76.1 1.0 CB C:HIS417 4.3 56.0 1.0 CB C:VAL414 4.3 48.8 1.0 CG C:HIS432 4.3 64.5 1.0 CA C:CYS415 4.4 53.6 1.0 O C:HIS428 4.6 58.5 1.0 CA C:CYS412 4.7 45.1 1.0 CG1 C:VAL414 4.8 50.1 1.0 C C:VAL414 4.8 54.6 1.0 N C:HIS417 4.9 55.4 1.0 CA C:VAL414 4.9 53.0 1.0

Zinc binding site 4 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220


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 Cc-220 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:66.8 occ:1.00 SG D:CYS326 2.3 71.9 1.0 SG D:CYS394 2.3 60.0 1.0 SG D:CYS391 2.4 61.5 1.0 SG D:CYS323 2.5 78.9 1.0 CB D:CYS391 3.1 54.5 1.0 CB D:CYS323 3.3 61.8 1.0 CB D:CYS394 3.5 60.3 1.0 CB D:CYS326 3.7 58.6 1.0 N D:CYS394 3.7 69.0 1.0 N D:CYS326 4.1 64.7 1.0 CA D:CYS394 4.2 67.5 1.0 OG1 D:THR329 4.3 69.5 1.0 CB D:ILE393 4.4 63.5 1.0 CA D:CYS326 4.5 61.3 1.0 CB D:THR329 4.5 56.1 1.0 CA D:CYS391 4.6 56.2 1.0 OG D:SER396 4.7 56.9 1.0 C D:ILE393 4.7 62.5 1.0 N D:ILE393 4.8 62.9 1.0 CA D:CYS323 4.8 62.8 1.0 CB D:GLN325 4.8 54.0 1.0 CA D:ILE393 4.8 62.0 1.0 C D:CYS394 4.9 69.2 1.0 N D:ALA395 5.0 63.5 1.0

Zinc binding site 5 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220


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 Cc-220 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:70.1 occ:1.00 NE2 F:HIS404 2.0 87.6 1.0 SG F:CYS384 2.3 88.0 1.0 CE1 F:HIS400 2.3 92.2 1.0 SG F:CYS387 2.4 87.0 1.0 CE1 F:HIS404 2.9 96.4 1.0 CD2 F:HIS404 3.0 102.0 1.0 CB F:CYS384 3.1 77.6 1.0 ND1 F:HIS400 3.1 91.5 1.0 NE2 F:HIS400 3.3 100.0 1.0 CB F:CYS387 3.4 69.5 1.0 N F:CYS387 3.9 87.4 1.0 ND1 F:HIS404 4.1 98.8 1.0 CG F:HIS404 4.1 100.9 1.0 CA F:CYS387 4.2 68.8 1.0 CG F:HIS400 4.3 105.6 1.0 CD2 F:HIS400 4.4 107.7 1.0 CA F:CYS384 4.6 78.8 1.0 O F:HIS400 4.6 114.5 1.0 CB F:TYR386 4.7 92.0 1.0 C F:TYR386 4.9 86.6 1.0 CD2 F:TYR386 4.9 100.2 1.0 C F:CYS387 5.0 72.7 1.0

Zinc binding site 6 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Short Bound to Cc-220


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 Cc-220 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:87.6 occ:1.00 NE2 F:HIS432 2.1 54.3 1.0 SG F:CYS415 2.3 53.0 1.0 SG F:CYS412 2.3 53.8 1.0 NE2 F:HIS428 2.4 75.4 1.0 CE1 F:HIS432 2.7 54.2 1.0 CD2 F:HIS428 2.8 66.0 1.0 CB F:CYS412 3.2 68.0 1.0 CD2 F:HIS432 3.3 55.7 1.0 CE1 F:HIS428 3.6 84.2 1.0 CB F:CYS415 3.7 55.6 1.0 ND1 F:HIS432 3.9 59.8 1.0 N F:CYS415 4.0 58.2 1.0 CG F:HIS428 4.1 74.4 1.0 CB F:HIS417 4.2 62.7 1.0 CG F:HIS432 4.2 56.6 1.0 ND1 F:HIS428 4.4 93.6 1.0 CA F:CYS415 4.4 58.0 1.0 CB F:VAL414 4.5 59.1 1.0 O F:HIS428 4.5 73.9 1.0 CA F:CYS412 4.7 55.8 1.0 N F:HIS417 4.8 68.1 1.0 C F:VAL414 5.0 60.5 1.0 CG1 F:VAL414 5.0 60.2 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