Zinc in PDB 8pql: K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide

Enzymatic activity of K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide

All present enzymatic activity of K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide:
2.3.2.23; 2.3.2.27; 2.3.2.32;

Zinc Binding Sites:

The binding sites of Zinc atom in the K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide (pdb code 8pql). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide, PDB code: 8pql:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8pql

Go back to Zinc Binding Sites List in 8pql
Zinc binding site 1 out of 3 in the K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor 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 K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn201

b:64.1
occ:1.00
 ND1 K:HIS80 2.0 73.3 1.0
SG K:CYS45 2.3 65.6 1.0
SG K:CYS42 2.3 68.3 1.0
SG K:CYS83 2.3 73.2 1.0
CG K:HIS80 2.6 73.3 1.0
CB K:CYS45 2.7 65.6 1.0
CE1 K:HIS80 2.8 73.3 1.0
CB K:HIS80 3.1 73.3 1.0
CB K:CYS42 3.3 68.3 1.0
N K:CYS45 3.4 65.6 1.0
CD2 K:HIS80 3.5 73.3 1.0
CA K:CYS45 3.5 65.6 1.0
NE2 K:HIS80 3.6 73.3 1.0
CB K:CYS83 3.8 73.2 1.0
C K:CYS45 4.3 65.6 1.0
CA K:HIS80 4.4 73.3 1.0
C K:ILE44 4.6 64.3 1.0
N K:ARG46 4.6 68.8 1.0
CA K:CYS42 4.7 68.3 1.0
CB K:ILE44 4.8 64.3 1.0
N K:ILE44 5.0 64.3 1.0

Zinc binding site 2 out of 3 in 8pql

Go back to Zinc Binding Sites List in 8pql
Zinc binding site 2 out of 3 in the K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor 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 K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn202

b:110.4
occ:1.00
 OD2 K:ASP97 2.0 74.3 1.0
ND1 K:HIS77 2.0 77.2 1.0
CE1 K:HIS77 2.2 77.2 1.0
SG K:CYS75 2.3 84.0 1.0
SG K:CYS94 2.3 73.9 1.0
CB K:CYS75 2.8 84.0 1.0
CG K:ASP97 3.1 74.3 1.0
CB K:CYS94 3.3 73.9 1.0
CG K:HIS77 3.4 77.2 1.0
NE2 K:HIS77 3.5 77.2 1.0
CB K:ASP97 3.8 74.3 1.0
CD2 K:HIS77 4.1 77.2 1.0
OD1 K:ASP97 4.1 74.3 1.0
CB K:HIS77 4.3 77.2 1.0
CA K:CYS75 4.3 84.0 1.0
CA K:CYS94 4.8 73.9 1.0
N K:CYS75 4.8 84.0 1.0
N K:ASP97 4.8 74.3 1.0
CA K:ASP97 4.9 74.3 1.0

Zinc binding site 3 out of 3 in 8pql

Go back to Zinc Binding Sites List in 8pql
Zinc binding site 3 out of 3 in the K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor 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 K48-Linked Ubiquitin Chain Formation with A Cullin-Ring E3 Ligase and CDC34: NEDD8-CUL2-RBX1-Elob/C-FEM1C with Trapped UBE2R2-Donor Ub- Acceptor Ub-SIL1 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn203

b:119.3
occ:1.00
 ND1 K:HIS82 2.0 69.9 1.0
SG K:CYS53 2.3 77.1 1.0
SG K:CYS56 2.3 78.5 1.0
SG K:CYS68 2.3 71.2 1.0
CE1 K:HIS82 2.7 69.9 1.0
CG K:HIS82 3.2 69.9 1.0
CB K:CYS53 3.3 77.1 1.0
CB K:CYS68 3.6 71.2 1.0
CB K:CYS56 3.7 78.5 1.0
CB K:HIS82 3.8 69.9 1.0
NE2 K:HIS82 3.8 69.9 1.0
CD2 K:HIS82 4.1 69.9 1.0
N K:CYS53 4.4 77.1 1.0
NE2 K:HIS80 4.5 73.3 1.0
CA K:CYS53 4.5 77.1 1.0
CA K:CYS56 4.8 78.5 1.0
CA K:CYS68 4.9 71.2 1.0
N K:CYS56 4.9 78.5 1.0
N K:HIS82 5.0 69.9 1.0
CA K:HIS82 5.0 69.9 1.0

Reference:

J.Liwocha, B.A.Schulman. Mechanism of Millisecond Poly-Ubiquitin Chain Formation By Cullin-Ring Ligases To Be Published 2024.
DOI: 10.1038/S41594-023-01206-1
Page generated: Thu Oct 31 09:46:08 2024

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