Zinc in PDB 6ttu: Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2

All present enzymatic activity of Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2:
2.3.2.23; 2.3.2.24; 2.3.2.27; 2.3.2.32;

The binding sites of Zinc atom in the Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2 (pdb code 6ttu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2, PDB code: 6ttu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2 within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:0.4 occ:1.00 ND1 R:HIS80 2.0 0.3 1.0 SG R:CYS42 2.3 0.7 1.0 SG R:CYS45 2.3 96.8 1.0 SG R:CYS83 2.3 0.6 1.0 CE1 R:HIS80 2.8 0.3 1.0 CG R:HIS80 3.1 0.3 1.0 CB R:CYS42 3.2 0.7 1.0 CB R:CYS83 3.6 0.6 1.0 CB R:HIS80 3.6 0.3 1.0 CB R:CYS45 3.9 96.8 1.0 N R:CYS45 3.9 96.8 1.0 NE2 R:HIS80 3.9 0.3 1.0 CD2 R:HIS80 4.1 0.3 1.0 CB R:ILE44 4.1 92.0 1.0 N R:HIS80 4.2 0.3 1.0 CA R:CYS45 4.5 96.8 1.0 CA R:HIS80 4.5 0.3 1.0 CA R:CYS42 4.7 0.7 1.0 CG1 R:ILE44 4.8 92.0 1.0 C R:ILE44 4.8 92.0 1.0 CG2 R:ILE44 4.9 92.0 1.0 CA R:ILE44 4.9 92.0 1.0 N R:ILE44 5.0 92.0 1.0

Zinc binding site 2 out of 3 in the Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2 within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn202 b:0.4 occ:1.00 OD2 R:ASP97 2.0 0.6 1.0 ND1 R:HIS77 2.0 0.8 1.0 SG R:CYS94 2.3 0.6 1.0 SG R:CYS75 2.3 0.5 1.0 CG R:ASP97 2.6 0.6 1.0 CE1 R:HIS77 2.6 0.8 1.0 OD1 R:ASP97 2.7 0.6 1.0 CB R:CYS75 2.8 0.5 1.0 CG R:HIS77 3.3 0.8 1.0 CB R:CYS94 3.6 0.6 1.0 NE2 R:HIS77 3.9 0.8 1.0 CB R:ASP97 3.9 0.6 1.0 CB R:HIS77 4.0 0.8 1.0 N R:ASP97 4.1 0.6 1.0 CD2 R:HIS77 4.2 0.8 1.0 CA R:CYS75 4.3 0.5 1.0 CB R:LEU96 4.4 0.9 1.0 CA R:ASP97 4.6 0.6 1.0 C R:LEU96 4.7 0.9 1.0 O R:ASP97 4.8 0.6 1.0 N R:CYS75 4.8 0.5 1.0 N R:LEU96 4.9 0.9 1.0 CA R:LEU96 4.9 0.9 1.0 CA R:CYS94 4.9 0.6 1.0 C R:CYS75 5.0 0.5 1.0

Zinc binding site 3 out of 3 in the Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase at 3.7A Resolution: NEDD8-CUL1-RBX1 N98R-SKP1-Monomeric B-TRCP1DD-Ikba- Ub~UBE2D2 within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn203 b:0.5 occ:1.00 ND1 R:HIS82 2.0 0.8 1.0 SG R:CYS68 2.3 0.0 1.0 CB R:CYS53 2.3 0.2 1.0 SG R:CYS53 2.3 0.2 1.0 SG R:CYS56 2.4 0.8 1.0 CB R:CYS56 2.7 0.8 1.0 CB R:CYS68 2.7 0.0 1.0 CE1 R:HIS82 2.8 0.8 1.0 CG R:HIS82 3.2 0.8 1.0 CB R:HIS82 3.7 0.8 1.0 CA R:CYS53 3.7 0.2 1.0 CA R:CYS68 3.8 0.0 1.0 CA R:CYS56 4.0 0.8 1.0 NE2 R:HIS82 4.0 0.8 1.0 N R:CYS53 4.2 0.2 1.0 N R:CYS56 4.2 0.8 1.0 CD2 R:HIS82 4.2 0.8 1.0 C R:CYS53 4.5 0.2 1.0 N R:CYS68 4.6 0.0 1.0 O R:CYS53 4.9 0.2 1.0 C R:CYS68 4.9 0.0 1.0 N R:HIS82 4.9 0.8 1.0 CA R:HIS82 5.0 0.8 1.0

K.Baek, D.T.Krist, J.R.Prabu, S.Hill, M.Kluegel, L.M.Neumaier, S.Von Gronau, G.Kleiger, B.A.Schulman. NEDD8 Nucleates A Multivalent Cullin-Ring-UBE2D Ubiquitin Ligation Assembly Nature 2020.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-020-2000-Y