Zinc in PDB 8tnp: Cryo-Em Structure of DDB1DB:Crbn:Pomalidomide:SD40

The binding sites of Zinc atom in the Cryo-Em Structure of DDB1DB:Crbn:Pomalidomide:SD40 (pdb code 8tnp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of DDB1DB:Crbn:Pomalidomide:SD40, PDB code: 8tnp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of DDB1DB:Crbn:Pomalidomide:SD40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of DDB1DB:Crbn:Pomalidomide:SD40 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:197.3 occ:1.00 SG B:CYS394 2.3 157.3 1.0 SG B:CYS391 2.3 153.8 1.0 SG B:CYS326 2.3 151.6 1.0 SG B:CYS323 2.3 149.0 1.0 HB3 B:CYS394 3.0 157.3 1.0 H B:CYS326 3.1 151.6 1.0 H B:CYS394 3.1 157.3 1.0 CB B:CYS394 3.2 157.3 1.0 HB3 B:CYS323 3.4 149.0 1.0 CB B:CYS323 3.4 149.0 1.0 HB2 B:CYS323 3.5 149.0 1.0 HB3 B:GLN325 3.5 151.9 1.0 HB2 B:CYS326 3.6 151.6 1.0 CB B:CYS326 3.6 151.6 1.0 N B:CYS394 3.8 157.3 1.0 N B:CYS326 3.8 151.6 1.0 CB B:CYS391 3.8 153.8 1.0 HB2 B:SER396 3.9 153.5 1.0 HB3 B:CYS391 3.9 153.8 1.0 CA B:CYS394 4.0 157.3 1.0 HB B:ILE393 4.0 152.1 1.0 H B:SER396 4.0 153.5 1.0 HB2 B:CYS394 4.0 157.3 1.0 HB2 B:CYS391 4.1 153.8 1.0 HG B:SER396 4.2 153.5 1.0 HD11 B:ILE398 4.3 147.0 1.0 CA B:CYS326 4.3 151.6 1.0 HB3 B:CYS326 4.4 151.6 1.0 CB B:GLN325 4.4 151.9 1.0 H B:ALA395 4.5 155.2 1.0 HB2 B:GLN325 4.5 151.9 1.0 H B:GLN325 4.5 151.9 1.0 C B:CYS394 4.5 157.3 1.0 H B:ILE393 4.6 152.1 1.0 OG B:SER396 4.6 153.5 1.0 CB B:SER396 4.7 153.5 1.0 HA B:CYS326 4.7 151.6 1.0 N B:ALA395 4.7 155.2 1.0 HG22 B:ILE393 4.7 152.1 1.0 C B:GLN325 4.8 151.9 1.0 N B:SER396 4.8 153.5 1.0 CA B:CYS323 4.8 149.0 1.0 C B:ILE393 4.8 152.1 1.0 HA B:CYS394 4.9 157.3 1.0 CB B:ILE393 4.9 152.1 1.0 HB B:THR329 4.9 148.6 1.0 HG1 B:THR329 5.0 148.6 1.0 CA B:GLN325 5.0 151.9 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of DDB1DB:Crbn:Pomalidomide:SD40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of DDB1DB:Crbn:Pomalidomide:SD40 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:190.0 occ:1.00 NE2 C:HIS35 2.0 167.1 1.0 NE2 C:HIS39 2.0 162.2 1.0 SG C:CYS22 2.3 158.9 1.0 SG C:CYS19 2.3 160.2 1.0 H C:CYS22 2.5 158.9 1.0 HB3 C:CYS22 2.5 158.9 1.0 CB C:CYS22 2.8 158.9 1.0 CE1 C:HIS35 2.9 167.1 1.0 CD2 C:HIS39 3.0 162.2 1.0 HE1 C:HIS35 3.0 167.1 1.0 HB C:ILE21 3.0 158.8 1.0 CE1 C:HIS39 3.1 162.2 1.0 CD2 C:HIS35 3.1 167.1 1.0 HD2 C:HIS39 3.1 162.2 1.0 N C:CYS22 3.1 158.9 1.0 HE1 C:HIS39 3.3 162.2 1.0 HD2 C:HIS35 3.3 167.1 1.0 HB3 C:CYS19 3.5 160.2 1.0 CB C:CYS19 3.5 160.2 1.0 CA C:CYS22 3.5 158.9 1.0 HB2 C:CYS22 3.7 158.9 1.0 HB2 C:CYS19 3.8 160.2 1.0 H C:PHE24 3.8 160.4 1.0 H C:ILE21 3.9 158.8 1.0 CB C:ILE21 4.0 158.8 1.0 ND1 C:HIS35 4.0 167.1 1.0 HB2 C:PHE24 4.1 160.4 1.0 HB3 C:PHE24 4.1 160.4 1.0 CG C:HIS35 4.1 167.1 1.0 CG C:HIS39 4.1 162.2 1.0 ND1 C:HIS39 4.1 162.2 1.0 H C:GLY23 4.2 156.9 1.0 C C:ILE21 4.2 158.8 1.0 HD12 C:ILE21 4.2 158.8 1.0 HB2 B:HIS397 4.3 148.7 1.0 HA C:CYS22 4.3 158.9 1.0 C C:CYS22 4.4 158.9 1.0 HG13 C:ILE21 4.4 158.8 1.0 CA C:ILE21 4.5 158.8 1.0 N C:GLY23 4.5 156.9 1.0 CB C:PHE24 4.5 160.4 1.0 N C:ILE21 4.5 158.8 1.0 CG1 C:ILE21 4.7 158.8 1.0 HA C:ILE36 4.7 166.0 1.0 HB3 B:HIS397 4.7 148.7 1.0 N C:PHE24 4.7 160.4 1.0 HD1 C:HIS35 4.7 167.1 1.0 HG13 C:ILE36 4.8 166.0 1.0 HG21 C:ILE21 4.8 158.8 1.0 CA C:CYS19 4.8 160.2 1.0 CB B:HIS397 4.9 148.7 1.0 CG2 C:ILE21 4.9 158.8 1.0 HD1 C:HIS39 4.9 162.2 1.0 CD1 C:ILE21 4.9 158.8 1.0 HG22 C:ILE21 4.9 158.8 1.0

S.S.Roy Burman, S.S.Roy Burman, M.Hunkeler, E.S.Fischer. N/A N/A.