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

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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 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 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 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 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

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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

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