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Zinc in PDB 8r5h: Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2

Enzymatic activity of Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2

All present enzymatic activity of Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2:
2.3.2.23;

Other elements in 8r5h:

The structure of Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2 (pdb code 8r5h). 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 Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2, PDB code: 8r5h:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8r5h

Go back to Zinc Binding Sites List in 8r5h
Zinc binding site 1 out of 3 in the Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2


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 Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:76.5
occ:1.00
 ND1 R:HIS80 2.0 77.1 1.0
SG R:CYS45 2.3 77.2 1.0
SG R:CYS42 2.3 67.3 1.0
SG R:CYS83 2.3 81.1 1.0
CG R:HIS80 2.9 77.1 1.0
CE1 R:HIS80 3.1 77.1 1.0
CB R:HIS80 3.1 77.1 1.0
CB R:CYS45 3.5 77.2 1.0
CB R:CYS42 3.5 67.3 1.0
N R:CYS45 3.7 77.2 1.0
CB R:CYS83 3.8 81.1 1.0
CD2 R:HIS80 4.1 77.1 1.0
CA R:CYS45 4.1 77.2 1.0
NE2 R:HIS80 4.2 77.1 1.0
CB R:ILE44 4.4 71.7 1.0
CA R:HIS80 4.7 77.1 1.0
C R:CYS45 4.7 77.2 1.0
C R:ILE44 4.8 71.7 1.0
N R:ARG46 4.9 70.7 1.0
CA R:CYS42 4.9 67.3 1.0
N R:ILE44 4.9 71.7 1.0
CA R:ILE44 5.0 71.7 1.0

Zinc binding site 2 out of 3 in 8r5h

Go back to Zinc Binding Sites List in 8r5h
Zinc binding site 2 out of 3 in the Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2


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 Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:90.9
occ:1.00
 OD2 R:ASP97 2.0 85.2 1.0
ND1 R:HIS77 2.0 74.1 1.0
SG R:CYS75 2.3 77.0 1.0
SG R:CYS94 2.3 78.8 1.0
CE1 R:HIS77 2.6 74.1 1.0
CG R:ASP97 3.0 85.2 1.0
CG R:HIS77 3.3 74.1 1.0
CB R:CYS94 3.4 78.8 1.0
CB R:ASP97 3.7 85.2 1.0
NE2 R:HIS77 3.9 74.1 1.0
CB R:CYS75 3.9 77.0 1.0
CB R:HIS77 3.9 74.1 1.0
OD1 R:ASP97 4.0 85.2 1.0
CD2 R:HIS77 4.2 74.1 1.0
N R:ASP97 4.6 85.2 1.0
CA R:ASP97 4.8 85.2 1.0
CA R:CYS94 4.9 78.8 1.0
N R:HIS77 5.0 74.1 1.0

Zinc binding site 3 out of 3 in 8r5h

Go back to Zinc Binding Sites List in 8r5h
Zinc binding site 3 out of 3 in the Ubiquitin Ligation to Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2


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 Neosubstrate By A Cullin-Ring E3 Ligase & CDC34: NEDD8-CUL2-RBX1-Elob/C-Vhl-MZ1 with Trapped UBE2R2~Donor Ub-BRD4 BD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn203

b:107.2
occ:1.00
 ND1 R:HIS82 2.0 84.4 1.0
SG R:CYS56 2.3 113.6 1.0
SG R:CYS53 2.3 104.3 1.0
SG R:CYS68 2.3 84.4 1.0
CE1 R:HIS82 2.9 84.4 1.0
CG R:HIS82 3.1 84.4 1.0
CB R:CYS53 3.3 104.3 1.0
CB R:CYS68 3.3 84.4 1.0
CB R:HIS82 3.6 84.4 1.0
CB R:CYS56 3.8 113.6 1.0
NE2 R:HIS82 4.0 84.4 1.0
N R:CYS53 4.1 104.3 1.0
CD2 R:HIS82 4.2 84.4 1.0
CA R:CYS53 4.3 104.3 1.0
CA R:CYS68 4.6 84.4 1.0
NE2 R:HIS80 4.7 77.1 1.0
N R:HIS82 4.7 84.4 1.0
CA R:HIS82 4.8 84.4 1.0
N R:CYS56 4.8 113.6 1.0
CA R:CYS56 4.9 113.6 1.0
N R:CYS68 4.9 84.4 1.0

Reference:

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
Page generated: Fri Aug 22 12:53:01 2025

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