Zinc in PDB 8rhz: Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
Enzymatic activity of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
All present enzymatic activity of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer:
2.3.2.27;
2.3.2.32;
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
(pdb code 8rhz). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer, PDB code: 8rhz:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 8rhz
Go back to
Zinc Binding Sites List in 8rhz
Zinc binding site 1 out
of 6 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:244.5
occ:1.00
|
SG
|
C:CYS42
|
2.2
|
224.4
|
1.0
|
ND1
|
C:HIS80
|
2.2
|
215.2
|
1.0
|
SG
|
C:CYS83
|
2.2
|
221.5
|
1.0
|
SG
|
C:CYS45
|
2.4
|
234.7
|
1.0
|
CE1
|
C:HIS80
|
2.7
|
215.2
|
1.0
|
CG
|
C:HIS80
|
2.9
|
215.2
|
1.0
|
CB
|
C:CYS45
|
3.2
|
234.7
|
1.0
|
CB
|
C:CYS42
|
3.3
|
224.4
|
1.0
|
NE2
|
C:HIS80
|
3.4
|
215.2
|
1.0
|
CB
|
C:HIS80
|
3.5
|
215.2
|
1.0
|
CD2
|
C:HIS80
|
3.5
|
215.2
|
1.0
|
CB
|
C:CYS83
|
3.8
|
221.5
|
1.0
|
N
|
C:CYS45
|
3.8
|
234.7
|
1.0
|
CG2
|
C:ILE44
|
3.9
|
232.9
|
1.0
|
CA
|
C:CYS45
|
4.0
|
234.7
|
1.0
|
O
|
C:CYS42
|
4.1
|
224.4
|
1.0
|
N
|
C:HIS80
|
4.2
|
215.2
|
1.0
|
CA
|
C:HIS80
|
4.5
|
215.2
|
1.0
|
CA
|
C:CYS42
|
4.6
|
224.4
|
1.0
|
C
|
C:CYS42
|
4.7
|
224.4
|
1.0
|
C
|
C:CYS45
|
4.7
|
234.7
|
1.0
|
SG
|
C:CYS53
|
4.8
|
222.8
|
1.0
|
N
|
C:ARG46
|
4.9
|
234.6
|
1.0
|
C
|
C:ILE44
|
5.0
|
232.9
|
1.0
|
|
Zinc binding site 2 out
of 6 in 8rhz
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Zinc Binding Sites List in 8rhz
Zinc binding site 2 out
of 6 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn202
b:238.4
occ:1.00
|
OD2
|
C:ASP97
|
1.8
|
233.7
|
1.0
|
ND1
|
C:HIS77
|
2.0
|
201.0
|
1.0
|
SG
|
C:CYS75
|
2.3
|
205.6
|
1.0
|
CE1
|
C:HIS77
|
2.3
|
201.0
|
1.0
|
SG
|
C:CYS94
|
2.5
|
237.0
|
1.0
|
CG
|
C:ASP97
|
2.6
|
233.7
|
1.0
|
OD1
|
C:ASP97
|
3.0
|
233.7
|
1.0
|
CB
|
C:CYS75
|
3.0
|
205.6
|
1.0
|
CG
|
C:HIS77
|
3.3
|
201.0
|
1.0
|
NE2
|
C:HIS77
|
3.5
|
201.0
|
1.0
|
CB
|
C:CYS94
|
3.6
|
237.0
|
1.0
|
CB
|
C:ASP97
|
3.8
|
233.7
|
1.0
|
O
|
C:CYS75
|
3.9
|
205.6
|
1.0
|
CD2
|
C:HIS77
|
4.0
|
201.0
|
1.0
|
CB
|
C:HIS77
|
4.1
|
201.0
|
1.0
|
N
|
C:ASP97
|
4.2
|
233.7
|
1.0
|
CA
|
C:CYS75
|
4.3
|
205.6
|
1.0
|
C
|
C:CYS75
|
4.3
|
205.6
|
1.0
|
CB
|
C:LEU96
|
4.3
|
233.2
|
1.0
|
CA
|
C:ASP97
|
4.6
|
233.7
|
1.0
|
C
|
C:LEU96
|
4.7
|
233.2
|
1.0
|
N
|
C:HIS77
|
4.8
|
201.0
|
1.0
|
CA
|
C:LEU96
|
4.9
|
233.2
|
1.0
|
N
|
C:LEU96
|
4.9
|
233.2
|
1.0
|
CG
|
C:LEU96
|
5.0
|
233.2
|
1.0
|
|
Zinc binding site 3 out
of 6 in 8rhz
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Zinc Binding Sites List in 8rhz
Zinc binding site 3 out
of 6 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn203
b:250.5
occ:1.00
|
CB
|
C:CYS53
|
1.8
|
222.8
|
1.0
|
ND1
|
C:HIS82
|
2.0
|
221.1
|
1.0
|
SG
|
C:CYS53
|
2.2
|
222.8
|
1.0
|
SG
|
C:CYS68
|
2.3
|
221.6
|
1.0
|
SG
|
C:CYS56
|
2.5
|
219.1
|
1.0
|
CG
|
C:HIS82
|
3.0
|
221.1
|
1.0
|
CE1
|
C:HIS82
|
3.0
|
221.1
|
1.0
|
CB
|
C:CYS68
|
3.0
|
221.6
|
1.0
|
CA
|
C:CYS53
|
3.3
|
222.8
|
1.0
|
CB
|
C:HIS82
|
3.3
|
221.1
|
1.0
|
N
|
C:CYS53
|
3.9
|
222.8
|
1.0
|
NE2
|
C:HIS82
|
4.0
|
221.1
|
1.0
|
CD2
|
C:HIS82
|
4.0
|
221.1
|
1.0
|
CB
|
C:CYS56
|
4.0
|
219.1
|
1.0
|
C
|
C:CYS53
|
4.0
|
222.8
|
1.0
|
CA
|
C:CYS68
|
4.2
|
221.6
|
1.0
|
O
|
C:CYS53
|
4.3
|
222.8
|
1.0
|
N
|
C:CYS68
|
4.4
|
221.6
|
1.0
|
N
|
C:CYS56
|
4.5
|
219.1
|
1.0
|
CA
|
C:HIS82
|
4.7
|
221.1
|
1.0
|
N
|
C:HIS82
|
4.9
|
221.1
|
1.0
|
CA
|
C:CYS56
|
4.9
|
219.1
|
1.0
|
CB
|
C:HIS80
|
4.9
|
215.2
|
1.0
|
N
|
C:ILE54
|
5.0
|
223.5
|
1.0
|
|
Zinc binding site 4 out
of 6 in 8rhz
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Zinc Binding Sites List in 8rhz
Zinc binding site 4 out
of 6 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn201
b:260.9
occ:1.00
|
ND1
|
D:HIS80
|
2.0
|
229.6
|
1.0
|
SG
|
D:CYS42
|
2.3
|
237.6
|
1.0
|
SG
|
D:CYS45
|
2.3
|
249.2
|
1.0
|
SG
|
D:CYS83
|
2.3
|
228.9
|
1.0
|
CE1
|
D:HIS80
|
2.5
|
229.6
|
1.0
|
CG
|
D:HIS80
|
2.7
|
229.6
|
1.0
|
CB
|
D:CYS45
|
3.3
|
249.2
|
1.0
|
NE2
|
D:HIS80
|
3.3
|
229.6
|
1.0
|
CB
|
D:CYS42
|
3.3
|
237.6
|
1.0
|
CD2
|
D:HIS80
|
3.4
|
229.6
|
1.0
|
CB
|
D:HIS80
|
3.4
|
229.6
|
1.0
|
CB
|
D:CYS83
|
3.9
|
228.9
|
1.0
|
N
|
D:CYS45
|
4.0
|
249.2
|
1.0
|
CA
|
D:CYS45
|
4.1
|
249.2
|
1.0
|
CG2
|
D:ILE44
|
4.2
|
245.7
|
1.0
|
N
|
D:HIS80
|
4.2
|
229.6
|
1.0
|
O
|
D:CYS42
|
4.2
|
237.6
|
1.0
|
CA
|
D:HIS80
|
4.5
|
229.6
|
1.0
|
CA
|
D:CYS42
|
4.6
|
237.6
|
1.0
|
SG
|
D:CYS53
|
4.6
|
237.2
|
1.0
|
C
|
D:CYS45
|
4.7
|
249.2
|
1.0
|
C
|
D:CYS42
|
4.8
|
237.6
|
1.0
|
N
|
D:ARG46
|
5.0
|
247.3
|
1.0
|
|
Zinc binding site 5 out
of 6 in 8rhz
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Zinc Binding Sites List in 8rhz
Zinc binding site 5 out
of 6 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn202
b:268.5
occ:1.00
|
OD2
|
D:ASP97
|
2.0
|
253.9
|
1.0
|
ND1
|
D:HIS77
|
2.0
|
231.0
|
1.0
|
SG
|
D:CYS75
|
2.3
|
229.5
|
1.0
|
SG
|
D:CYS94
|
2.3
|
245.8
|
1.0
|
CE1
|
D:HIS77
|
2.4
|
231.0
|
1.0
|
CG
|
D:ASP97
|
2.7
|
253.9
|
1.0
|
OD1
|
D:ASP97
|
3.0
|
253.9
|
1.0
|
CB
|
D:CYS75
|
3.2
|
229.5
|
1.0
|
CG
|
D:HIS77
|
3.3
|
231.0
|
1.0
|
CB
|
D:CYS94
|
3.5
|
245.8
|
1.0
|
NE2
|
D:HIS77
|
3.6
|
231.0
|
1.0
|
CB
|
D:ASP97
|
3.9
|
253.9
|
1.0
|
CD2
|
D:HIS77
|
4.1
|
231.0
|
1.0
|
CB
|
D:HIS77
|
4.1
|
231.0
|
1.0
|
O
|
D:CYS75
|
4.1
|
229.5
|
1.0
|
N
|
D:ASP97
|
4.1
|
253.9
|
1.0
|
CB
|
D:LEU96
|
4.2
|
247.3
|
1.0
|
CA
|
D:CYS75
|
4.4
|
229.5
|
1.0
|
C
|
D:CYS75
|
4.4
|
229.5
|
1.0
|
CA
|
D:ASP97
|
4.6
|
253.9
|
1.0
|
C
|
D:LEU96
|
4.7
|
247.3
|
1.0
|
N
|
D:LEU96
|
4.8
|
247.3
|
1.0
|
CA
|
D:LEU96
|
4.8
|
247.3
|
1.0
|
N
|
D:HIS77
|
4.8
|
231.0
|
1.0
|
CA
|
D:CYS94
|
4.9
|
245.8
|
1.0
|
CE2
|
D:PHE79
|
4.9
|
226.0
|
1.0
|
CG
|
D:LEU96
|
4.9
|
247.3
|
1.0
|
|
Zinc binding site 6 out
of 6 in 8rhz
Go back to
Zinc Binding Sites List in 8rhz
Zinc binding site 6 out
of 6 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated Conformation - Symmetry Expanded Unneddylated Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn203
b:253.3
occ:1.00
|
CB
|
D:CYS53
|
1.8
|
237.2
|
1.0
|
ND1
|
D:HIS82
|
2.0
|
229.1
|
1.0
|
SG
|
D:CYS56
|
2.3
|
236.7
|
1.0
|
SG
|
D:CYS68
|
2.3
|
228.8
|
1.0
|
SG
|
D:CYS53
|
2.3
|
237.2
|
1.0
|
CE1
|
D:HIS82
|
2.9
|
229.1
|
1.0
|
CB
|
D:CYS68
|
3.0
|
228.8
|
1.0
|
CG
|
D:HIS82
|
3.0
|
229.1
|
1.0
|
CA
|
D:CYS53
|
3.3
|
237.2
|
1.0
|
CB
|
D:HIS82
|
3.4
|
229.1
|
1.0
|
N
|
D:CYS53
|
3.9
|
237.2
|
1.0
|
CB
|
D:CYS56
|
3.9
|
236.7
|
1.0
|
NE2
|
D:HIS82
|
4.0
|
229.1
|
1.0
|
C
|
D:CYS53
|
4.0
|
237.2
|
1.0
|
CD2
|
D:HIS82
|
4.1
|
229.1
|
1.0
|
O
|
D:CYS53
|
4.2
|
237.2
|
1.0
|
CA
|
D:CYS68
|
4.2
|
228.8
|
1.0
|
N
|
D:CYS68
|
4.3
|
228.8
|
1.0
|
N
|
D:CYS56
|
4.4
|
236.7
|
1.0
|
CA
|
D:CYS56
|
4.8
|
236.7
|
1.0
|
CA
|
D:HIS82
|
4.8
|
229.1
|
1.0
|
N
|
D:ILE54
|
5.0
|
238.7
|
1.0
|
|
Reference:
L.V.M.Hopf,
D.Horn-Ghetko,
B.A.Schulman.
Noncanonical Assembly, Neddylation and Chimeric Cullin Ring/Rbr Ubiquitylation By the 1.8 Mda CUL9 E3 Ligase Complex Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01257-Y
Page generated: Thu Oct 31 10:31:14 2024
|