Zinc in PDB 8q7r: Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide

All present enzymatic activity of Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide:
2.3.2.23; 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 & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide (pdb code 8q7r). 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 & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide, PDB code: 8q7r:
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 & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide


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 & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:64.1 occ:1.00 ND1 R:HIS80 2.0 73.3 1.0 SG R:CYS45 2.3 65.6 1.0 SG R:CYS42 2.3 68.3 1.0 SG R:CYS83 2.3 73.2 1.0 CG R:HIS80 2.6 73.3 1.0 CB R:CYS45 2.7 65.6 1.0 CE1 R:HIS80 2.8 73.3 1.0 CB R:HIS80 3.1 73.3 1.0 CB R:CYS42 3.3 68.3 1.0 N R:CYS45 3.4 65.6 1.0 CD2 R:HIS80 3.5 73.3 1.0 CA R:CYS45 3.5 65.6 1.0 NE2 R:HIS80 3.6 73.3 1.0 CB R:CYS83 3.8 73.2 1.0 C R:CYS45 4.3 65.6 1.0 CA R:HIS80 4.4 73.3 1.0 C R:ILE44 4.6 64.3 1.0 N R:ARG46 4.6 68.8 1.0 CA R:CYS42 4.7 68.3 1.0 CB R:ILE44 4.8 64.3 1.0 N R:ILE44 5.0 64.3 1.0

Zinc binding site 2 out of 3 in the Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide


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 & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn202 b:110.4 occ:1.00 OD2 R:ASP97 2.0 74.3 1.0 ND1 R:HIS77 2.0 77.2 1.0 CE1 R:HIS77 2.2 77.2 1.0 SG R:CYS75 2.3 84.0 1.0 SG R:CYS94 2.3 73.9 1.0 CB R:CYS75 2.8 84.0 1.0 CG R:ASP97 3.1 74.3 1.0 CB R:CYS94 3.3 73.9 1.0 CG R:HIS77 3.4 77.2 1.0 NE2 R:HIS77 3.5 77.2 1.0 CB R:ASP97 3.8 74.3 1.0 CD2 R:HIS77 4.1 77.2 1.0 OD1 R:ASP97 4.1 74.3 1.0 CA R:CYS75 4.3 84.0 1.0 CB R:HIS77 4.3 77.2 1.0 CA R:CYS94 4.8 73.9 1.0 N R:CYS75 4.8 84.0 1.0 N R:ASP97 4.8 74.3 1.0 CA R:ASP97 4.9 74.3 1.0

Zinc binding site 3 out of 3 in the Ubiquitin Ligation to Substrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide


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 & CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2~Donor Ub-SIL1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn203 b:119.3 occ:1.00 ND1 R:HIS82 2.0 69.9 1.0 SG R:CYS53 2.3 77.1 1.0 SG R:CYS56 2.3 78.5 1.0 SG R:CYS68 2.3 71.2 1.0 CE1 R:HIS82 2.7 69.9 1.0 CG R:HIS82 3.2 69.9 1.0 CB R:CYS53 3.3 77.1 1.0 CB R:CYS68 3.6 71.2 1.0 CB R:CYS56 3.7 78.5 1.0 CB R:HIS82 3.8 69.9 1.0 NE2 R:HIS82 3.8 69.9 1.0 CD2 R:HIS82 4.1 69.9 1.0 N R:CYS53 4.4 77.1 1.0 NE2 R:HIS80 4.5 73.3 1.0 CA R:CYS53 4.5 77.1 1.0 CA R:CYS56 4.8 78.5 1.0 CA R:CYS68 4.9 71.2 1.0 N R:CYS56 4.9 78.5 1.0 N R:HIS82 5.0 69.9 1.0 CA R:HIS82 5.0 69.9 1.0

J.Liwocha, J.R.Prabu, G.Kleiger, B.A.Schulman. Cullin-Ring Ligases Target Substrates with Geometrically Optimized Catalytic Partners Mol.Cell 2024.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2024.01.022