Zinc in PDB 8u17: The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long Bound to Pomalidomide

The structure of The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long Bound to Pomalidomide, PDB code: 8u17 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)	49.90 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.077, 151.66, 195.379, 90, 90, 90
R / Rfree (%)	30.5 / 34.6

The binding sites of Zinc atom in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long Bound to Pomalidomide (pdb code 8u17). 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)-Long Bound to Pomalidomide, PDB code: 8u17:
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)-Long 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)-Long Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:121.9 occ:1.00 SG A:CYS326 2.3 129.1 1.0 SG A:CYS394 2.3 140.7 1.0 SG A:CYS323 2.3 170.8 1.0 SG A:CYS391 2.3 121.9 1.0 CB A:CYS391 3.1 119.6 1.0 CB A:CYS323 3.2 130.1 1.0 CB A:CYS326 3.3 133.3 1.0 CB A:CYS394 3.7 131.3 1.0 N A:CYS326 3.9 117.6 1.0 N A:CYS394 4.0 136.8 1.0 OG1 A:THR329 4.1 163.2 1.0 CA A:CYS326 4.2 134.3 1.0 CA A:CYS394 4.4 133.9 1.0 CA A:CYS391 4.6 133.5 1.0 C A:GLN325 4.6 132.5 1.0 CA A:CYS323 4.6 120.3 1.0 CB A:GLN325 4.9 124.7 1.0 CB A:ILE393 4.9 174.2 1.0 N A:ALA395 4.9 141.3 1.0 C A:CYS323 4.9 118.9 1.0 C A:CYS394 4.9 146.2 1.0 N A:GLN325 4.9 128.5 1.0 CB A:SER396 4.9 114.3 1.0 N A:ILE393 5.0 166.2 1.0 N A:SER396 5.0 147.2 1.0

Zinc binding site 2 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long 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)-Long Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:129.2 occ:1.00 NE2 C:HIS404 2.1 122.7 1.0 NE2 C:HIS400 2.1 114.9 1.0 SG C:CYS387 2.3 182.4 1.0 SG C:CYS384 2.3 120.3 1.0 CD2 C:HIS404 2.9 141.4 1.0 CD2 C:HIS400 2.9 128.4 1.0 CE1 C:HIS400 3.0 114.2 1.0 CE1 C:HIS404 3.1 120.2 1.0 CB C:CYS384 3.5 131.7 1.0 N C:CYS387 3.6 167.5 1.0 CB C:CYS387 3.7 163.5 1.0 CG C:HIS400 4.0 146.0 1.0 ND1 C:HIS400 4.0 144.0 1.0 CG C:HIS404 4.1 149.2 1.0 CB C:TYR386 4.1 166.0 1.0 CA C:CYS387 4.2 168.0 1.0 ND1 C:HIS404 4.2 132.6 1.0 CD2 C:TYR386 4.6 155.5 1.0 C C:TYR386 4.7 163.2 1.0 N C:TYR386 4.7 173.9 1.0 CA C:TYR386 4.8 172.5 1.0 CB C:LYS389 4.8 126.8 1.0 N C:SER388 4.8 143.1 1.0 C C:CYS387 4.8 166.4 1.0 CG C:TYR386 4.9 156.3 1.0 CA C:CYS384 4.9 125.4 1.0 N C:LYS389 4.9 125.2 1.0

Zinc binding site 3 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long 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)-Long Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:105.7 occ:1.00 NE2 C:HIS428 2.0 148.7 1.0 NE2 C:HIS432 2.1 145.1 1.0 SG C:CYS415 2.3 121.1 1.0 SG C:CYS412 2.3 155.3 1.0 CD2 C:HIS432 2.4 131.2 1.0 CE1 C:HIS428 2.9 156.6 1.0 CD2 C:HIS428 3.0 125.1 1.0 CE1 C:HIS432 3.1 153.8 1.0 CB C:CYS415 3.2 122.1 1.0 CB C:CYS412 3.3 142.1 1.0 CG C:HIS432 3.5 136.2 1.0 N C:CYS415 3.6 121.2 1.0 ND1 C:HIS432 3.8 152.5 1.0 ND1 C:HIS428 3.9 156.1 1.0 CA C:CYS415 3.9 121.3 1.0 CG C:HIS428 4.0 121.7 1.0 CB C:VAL414 4.3 125.6 1.0 CB C:HIS417 4.4 144.5 1.0 C C:VAL414 4.6 121.6 1.0 C C:CYS415 4.6 137.6 1.0 CA C:CYS412 4.7 121.9 1.0 CB C:HIS432 4.7 122.8 1.0 CA C:VAL414 4.8 121.8 1.0 N C:VAL414 4.9 161.1 1.0 N C:HIS417 4.9 134.1 1.0 O C:HIS428 4.9 130.9 1.0 N C:GLY416 4.9 144.4 1.0 CG1 C:VAL414 5.0 153.7 1.0

Zinc binding site 4 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long 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)-Long Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:139.4 occ:1.00 SG D:CYS391 2.3 135.5 1.0 SG D:CYS394 2.3 135.6 1.0 SG D:CYS326 2.3 139.9 1.0 CB D:CYS391 2.9 136.1 1.0 SG D:CYS323 3.2 153.5 1.0 CB D:CYS323 3.4 126.0 1.0 CB D:CYS326 3.5 136.5 1.0 CB D:CYS394 3.5 164.7 1.0 N D:CYS394 3.9 164.2 1.0 OG1 D:THR329 4.2 153.6 1.0 CB D:THR329 4.2 134.6 1.0 CA D:CYS394 4.3 164.4 1.0 CA D:CYS391 4.4 147.7 1.0 CG2 D:THR329 4.7 136.7 1.0 CB D:ILE393 4.7 156.1 1.0 CA D:CYS326 4.8 152.7 1.0 N D:ILE393 4.8 156.1 1.0 N D:ALA395 4.8 145.7 1.0 C D:CYS394 4.9 146.1 1.0 C D:ILE393 4.9 164.7 1.0 N D:CYS326 4.9 160.9 1.0 CA D:CYS323 4.9 116.1 1.0

Zinc binding site 5 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long 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)-Long Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:143.4 occ:1.00 NE2 F:HIS404 2.1 115.6 1.0 NE2 F:HIS400 2.1 114.3 1.0 SG F:CYS387 2.3 123.3 1.0 SG F:CYS384 2.3 108.4 1.0 CD2 F:HIS404 2.9 127.5 1.0 CE1 F:HIS400 3.0 117.2 1.0 CD2 F:HIS400 3.1 129.8 1.0 CE1 F:HIS404 3.2 116.8 1.0 CB F:CYS384 3.6 116.5 1.0 N F:CYS387 3.9 149.7 1.0 CB F:CYS387 3.9 135.0 1.0 ND1 F:HIS400 4.1 129.2 1.0 CG F:HIS404 4.1 130.7 1.0 CG F:HIS400 4.2 138.4 1.0 CB F:TYR386 4.2 132.8 1.0 ND1 F:HIS404 4.2 131.5 1.0 CA F:CYS387 4.4 124.1 1.0 CB F:LYS389 4.7 97.1 1.0 CD2 F:TYR386 4.8 164.8 1.0 N F:TYR386 4.8 132.2 1.0 C F:TYR386 4.9 169.7 1.0 CA F:TYR386 4.9 154.5 1.0 N F:SER388 4.9 119.8 1.0 N F:LYS389 5.0 91.4 1.0 C F:CYS387 5.0 112.2 1.0

Zinc binding site 6 out of 6 in the The Ternary Complex Structure of DDB1-Crbn-SALL4(ZF1,2)-Long 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)-Long Bound to Pomalidomide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:140.7 occ:1.00 NE2 F:HIS428 2.1 184.8 1.0 NE2 F:HIS432 2.1 189.4 1.0 SG F:CYS415 2.3 107.5 1.0 SG F:CYS412 2.3 142.3 1.0 CD2 F:HIS428 2.5 176.4 1.0 CE1 F:HIS432 2.8 182.8 1.0 CD2 F:HIS432 3.2 198.1 1.0 CB F:CYS412 3.3 141.4 1.0 CE1 F:HIS428 3.3 187.9 1.0 CB F:CYS415 3.6 150.4 1.0 N F:CYS415 3.7 102.0 1.0 CG F:HIS428 3.8 163.8 1.0 ND1 F:HIS432 4.0 186.9 1.0 CB F:VAL414 4.1 97.3 1.0 ND1 F:HIS428 4.2 171.5 1.0 CG F:HIS432 4.2 196.6 1.0 CA F:CYS415 4.2 127.8 1.0 CG1 F:VAL414 4.6 143.5 1.0 C F:VAL414 4.6 98.7 1.0 CA F:CYS412 4.7 138.9 1.0 CA F:VAL414 4.7 97.2 1.0 O F:HIS428 4.7 156.4 1.0 N F:VAL414 4.7 113.1 1.0 CB F:HIS417 4.8 189.7 1.0 C F:CYS415 5.0 144.7 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