Zinc in PDB 6uml: Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex

The structure of Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex, PDB code: 6uml was solved by T.L.Clayton, M.E.Matyskiela, B.E.Pagarigan, E.T.Tran, P.P.Chamberlain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.70 / 3.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.409, 127.725, 110.174, 90.00, 109.69, 90.00
R / Rfree (%)	20.4 / 26.7

The binding sites of Zinc atom in the Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex (pdb code 6uml). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex, PDB code: 6uml:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:67.2 occ:1.00 SG C:CYS394 2.2 82.6 1.0 SG C:CYS326 2.3 84.8 1.0 SG C:CYS323 2.5 66.2 1.0 SG C:CYS391 2.5 57.3 1.0 CB C:CYS394 3.1 80.5 1.0 CB C:CYS326 3.1 89.6 1.0 CB C:CYS391 3.3 52.3 1.0 CB C:CYS323 3.5 67.9 1.0 N C:CYS326 3.6 93.4 1.0 N C:CYS394 3.7 61.1 1.0 CA C:CYS326 3.9 97.6 1.0 CA C:CYS394 4.0 72.0 1.0 CB C:GLN325 4.4 93.1 1.0 CB C:ILE393 4.6 60.1 1.0 C C:GLN325 4.7 87.6 1.0 CG C:GLN325 4.8 99.2 1.0 C C:CYS326 4.8 0.8 1.0 CA C:CYS391 4.8 51.2 1.0 C C:ILE393 4.8 64.6 1.0 C C:CYS394 4.8 79.5 1.0 CB C:THR329 4.9 95.0 1.0 CA C:CYS323 4.9 68.1 1.0 OG1 C:THR329 4.9 0.8 1.0 CA C:GLN325 5.0 86.8 1.0

Zinc binding site 2 out of 2 in the Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Thalidomide Teratogenicity Revealed By the Cereblon-DDB1-SALL4-Pomalidomide Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:87.5 occ:1.00 NE2 E:HIS428 2.1 0.2 1.0 SG E:CYS412 2.3 0.5 1.0 SG E:CYS415 2.5 91.9 1.0 CD2 E:HIS428 2.9 0.2 1.0 NE2 E:HIS432 3.0 0.4 1.0 CB E:CYS412 3.1 0.6 1.0 CE1 E:HIS428 3.2 0.8 1.0 CD2 E:HIS432 3.3 0.2 1.0 CB E:CYS415 3.7 77.6 1.0 N E:CYS415 3.9 68.5 1.0 CG E:HIS428 4.1 0.0 1.0 ND1 E:HIS428 4.2 0.5 1.0 CE1 E:HIS432 4.2 0.5 1.0 CA E:CYS415 4.4 73.4 1.0 CB E:VAL414 4.4 84.4 1.0 CB E:HIS417 4.5 79.5 1.0 CA E:CYS412 4.6 0.4 1.0 CG E:HIS432 4.7 0.5 1.0 N E:VAL414 4.8 91.6 1.0 C E:VAL414 4.8 68.1 1.0 CA E:VAL414 4.9 83.6 1.0 N E:GLY416 4.9 78.7 1.0 N E:HIS417 5.0 76.3 1.0

M.E.Matyskiela, T.Clayton, X.Zheng, C.Mayne, E.Tran, A.Carpenter, B.Pagarigan, J.Mcdonald, M.Rolfe, L.G.Hamann, G.Lu, P.P.Chamberlain. Crystal Structure of the SALL4-Pomalidomide-Cereblon-DDB1 Complex. Nat.Struct.Mol.Biol. 2020.
ISSN: ESSN 1545-9985
PubMed: 32251415
DOI: 10.1038/S41594-020-0405-9