Zinc in PDB 8q7h: Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer

Enzymatic activity of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer

All present enzymatic activity of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin 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 and Neddylated Conformation - Focused Cullin Dimer (pdb code 8q7h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer, PDB code: 8q7h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8q7h

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Zinc binding site 1 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin 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 and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2601

b:252.5
occ:1.00
 ND1 A:HIS2090 2.0 226.1 1.0
CB A:CYS2120 2.2 231.2 1.0
CE1 A:HIS2090 2.3 226.1 1.0
SG A:CYS2115 2.3 227.3 1.0
SG A:CYS2088 2.3 223.7 1.0
SG A:CYS2120 2.3 231.2 1.0
CB A:CYS2115 3.1 227.3 1.0
CG A:HIS2090 3.1 226.1 1.0
O A:CYS2088 3.2 223.7 1.0
NE2 A:HIS2090 3.3 226.1 1.0
CA A:CYS2120 3.7 231.2 1.0
CD2 A:HIS2090 3.8 226.1 1.0
CB A:ILE2117 3.9 224.0 1.0
CB A:CYS2088 3.9 223.7 1.0
CB A:HIS2090 4.0 226.1 1.0
C A:CYS2088 4.2 223.7 1.0
O A:CYS2120 4.2 231.2 1.0
O A:ILE2117 4.3 224.0 1.0
C A:CYS2120 4.4 231.2 1.0
CA A:CYS2088 4.5 223.7 1.0
CA A:CYS2115 4.5 227.3 1.0
N A:CYS2088 4.6 223.7 1.0
N A:CYS2120 4.6 231.2 1.0
CA A:ILE2117 4.8 224.0 1.0
C A:ILE2117 4.8 224.0 1.0
N A:ILE2117 4.9 224.0 1.0
O A:CYS2115 4.9 227.3 1.0
C A:CYS2115 4.9 227.3 1.0

Zinc binding site 2 out of 10 in 8q7h

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Zinc binding site 2 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin 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 and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2602

b:260.2
occ:1.00
 SG A:CYS2093 2.3 225.2 1.0
SG A:CYS2073 2.3 220.8 1.0
SG A:CYS2096 2.3 223.4 1.0
SG A:CYS2070 2.3 214.9 1.0
CB A:CYS2096 2.9 223.4 1.0
CB A:CYS2073 3.1 220.8 1.0
N A:CYS2096 3.5 223.4 1.0
N A:CYS2073 3.6 220.8 1.0
CB A:CYS2070 3.7 214.9 1.0
CB A:CYS2093 3.7 225.2 1.0
CA A:CYS2096 3.8 223.4 1.0
CA A:CYS2073 4.0 220.8 1.0
O A:CYS2093 4.0 225.2 1.0
N A:CYS2093 4.2 225.2 1.0
CB A:VAL2072 4.3 209.5 1.0
CA A:CYS2093 4.3 225.2 1.0
C A:CYS2093 4.4 225.2 1.0
C A:VAL2072 4.5 209.5 1.0
C A:SER2095 4.6 218.7 1.0
CB A:SER2095 4.6 218.7 1.0
CA A:VAL2072 4.8 209.5 1.0
N A:SER2095 4.8 218.7 1.0
O A:CYS2073 4.9 220.8 1.0
CA A:SER2095 4.9 218.7 1.0
C A:CYS2073 4.9 220.8 1.0
C A:CYS2096 5.0 223.4 1.0
N A:VAL2072 5.0 209.5 1.0

Zinc binding site 3 out of 10 in 8q7h

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Zinc binding site 3 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin 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 and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2603

b:190.2
occ:1.00
 NE2 A:HIS2198 2.0 146.3 1.0
SG A:CYS2192 2.3 153.0 1.0
SG A:CYS2189 2.3 151.7 1.0
SG A:CYS2203 2.3 153.6 1.0
CE1 A:HIS2198 2.4 146.3 1.0
CB A:CYS2203 3.2 153.6 1.0
CB A:CYS2192 3.3 153.0 1.0
CD2 A:HIS2198 3.3 146.3 1.0
N A:CYS2192 3.4 153.0 1.0
ND1 A:HIS2198 3.7 146.3 1.0
CB A:CYS2189 3.7 151.7 1.0
CA A:CYS2203 3.8 153.6 1.0
CA A:CYS2192 3.8 153.0 1.0
O A:CYS2192 4.1 153.0 1.0
CG A:HIS2198 4.2 146.3 1.0
CB A:ASN2191 4.3 145.0 1.0
C A:CYS2192 4.3 153.0 1.0
N A:CYS2203 4.4 153.6 1.0
C A:ASN2191 4.5 145.0 1.0
CA A:ASN2191 4.8 145.0 1.0
N A:ASN2191 4.9 145.0 1.0
CA A:CYS2189 5.0 151.7 1.0

Zinc binding site 4 out of 10 in 8q7h

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Zinc binding site 4 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin 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 and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2604

b:218.4
occ:1.00
 SG A:CYS2181 2.3 174.3 1.0
SG A:CYS2160 2.3 150.8 1.0
SG A:CYS2184 2.3 175.5 1.0
SG A:CYS2166 2.3 163.1 1.0
CB A:CYS2181 2.9 174.3 1.0
CB A:CYS2160 3.4 150.8 1.0
CB A:CYS2166 3.9 163.1 1.0
CB A:CYS2184 3.9 175.5 1.0
OD1 A:ASN2162 4.1 148.5 1.0
N A:CYS2184 4.2 175.5 1.0
ND2 A:ASN2162 4.4 148.5 1.0
CA A:CYS2181 4.4 174.3 1.0
CA A:CYS2184 4.6 175.5 1.0
CG A:ASN2162 4.7 148.5 1.0
CA A:CYS2166 4.8 163.1 1.0
CA A:CYS2160 4.8 150.8 1.0
CB A:LYS2183 4.8 175.1 1.0
N A:CYS2166 4.8 163.1 1.0
O A:CYS2166 4.8 163.1 1.0
CB A:ARG2168 4.9 147.8 1.0
C A:CYS2166 5.0 163.1 1.0

Zinc binding site 5 out of 10 in 8q7h

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Zinc binding site 5 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin 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 and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:142.2
occ:1.00
 ND1 C:HIS80 2.0 133.9 1.0
SG C:CYS45 2.3 120.7 1.0
SG C:CYS42 2.3 121.3 1.0
SG C:CYS83 2.3 142.4 1.0
CE1 C:HIS80 2.9 133.9 1.0
CB C:CYS42 3.0 121.3 1.0
CB C:CYS45 3.1 120.7 1.0
CG C:HIS80 3.1 133.9 1.0
CB C:CYS83 3.6 142.4 1.0
CB C:HIS80 3.6 133.9 1.0
N C:CYS45 3.8 120.7 1.0
CA C:CYS45 4.0 120.7 1.0
NE2 C:HIS80 4.0 133.9 1.0
CD2 C:HIS80 4.2 133.9 1.0
N C:HIS80 4.3 133.9 1.0
CA C:CYS42 4.5 121.3 1.0
CA C:HIS80 4.6 133.9 1.0
C C:CYS45 4.7 120.7 1.0
CB C:CYS53 4.8 136.8 1.0
C C:CYS42 4.8 121.3 1.0
C C:ILE44 4.8 116.2 1.0
O C:CYS42 4.9 121.3 1.0
CB C:ILE44 4.9 116.2 1.0
N C:ARG46 4.9 118.5 1.0
CA C:CYS83 4.9 142.4 1.0
N C:ILE44 5.0 116.2 1.0

Zinc binding site 6 out of 10 in 8q7h

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Zinc binding site 6 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin 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 and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:156.4
occ:1.00
 OD2 C:ASP97 2.0 126.9 1.0
ND1 C:HIS77 2.0 127.0 1.0
SG C:CYS75 2.3 129.3 1.0
SG C:CYS94 2.3 138.8 1.0
CG C:ASP97 2.6 126.9 1.0
CE1 C:HIS77 2.7 127.0 1.0
CB C:CYS75 2.8 129.3 1.0
OD1 C:ASP97 2.9 126.9 1.0
CG C:HIS77 3.1 127.0 1.0
CB C:CYS94 3.4 138.8 1.0
CB C:HIS77 3.7 127.0 1.0
NE2 C:HIS77 3.8 127.0 1.0
CB C:ASP97 3.8 126.9 1.0
CD2 C:HIS77 4.0 127.0 1.0
CA C:CYS75 4.2 129.3 1.0
CB C:LEU96 4.4 128.1 1.0
N C:ASP97 4.4 126.9 1.0
CZ3 C:TRP101 4.5 129.4 1.0
C C:CYS75 4.6 129.3 1.0
O C:CYS75 4.7 129.3 1.0
CA C:CYS94 4.8 138.8 1.0
CA C:ASP97 4.8 126.9 1.0
N C:HIS77 4.9 127.0 1.0
N C:LEU96 4.9 128.1 1.0
CA C:HIS77 4.9 127.0 1.0
C C:LEU96 4.9 128.1 1.0
CE3 C:TRP101 4.9 129.4 1.0
N C:CYS75 4.9 129.3 1.0
CA C:LEU96 5.0 128.1 1.0

Zinc binding site 7 out of 10 in 8q7h

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Zinc binding site 7 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:165.2
occ:1.00
 ND1 C:HIS82 2.0 138.0 1.0
SG C:CYS53 2.3 136.8 1.0
SG C:CYS56 2.3 137.8 1.0
SG C:CYS68 2.3 125.3 1.0
CE1 C:HIS82 2.7 138.0 1.0
CB C:CYS56 3.1 137.8 1.0
CG C:HIS82 3.2 138.0 1.0
CB C:CYS53 3.3 136.8 1.0
CB C:CYS68 3.5 125.3 1.0
CB C:HIS82 3.8 138.0 1.0
NE2 C:HIS82 3.9 138.0 1.0
N C:CYS53 4.0 136.8 1.0
N C:CYS56 4.0 137.8 1.0
CA C:CYS53 4.1 136.8 1.0
CD2 C:HIS82 4.2 138.0 1.0
CA C:CYS56 4.2 137.8 1.0
CA C:CYS68 4.4 125.3 1.0
C C:CYS53 4.6 136.8 1.0
O C:CYS53 4.6 136.8 1.0

Zinc binding site 8 out of 10 in 8q7h

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Zinc binding site 8 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:193.0
occ:1.00
 ND1 D:HIS80 2.0 161.8 1.0
SG D:CYS42 2.3 160.3 1.0
SG D:CYS45 2.3 172.9 1.0
SG D:CYS83 2.3 153.1 1.0
CE1 D:HIS80 2.5 161.8 1.0
CG D:HIS80 2.7 161.8 1.0
CB D:CYS45 3.3 172.9 1.0
NE2 D:HIS80 3.3 161.8 1.0
CB D:CYS42 3.3 160.3 1.0
CD2 D:HIS80 3.4 161.8 1.0
CB D:HIS80 3.4 161.8 1.0
CB D:CYS83 3.9 153.1 1.0
N D:CYS45 4.0 172.9 1.0
CA D:CYS45 4.1 172.9 1.0
CG2 D:ILE44 4.2 159.0 1.0
N D:HIS80 4.2 161.8 1.0
O D:CYS42 4.2 160.3 1.0
CA D:HIS80 4.5 161.8 1.0
CA D:CYS42 4.6 160.3 1.0
SG D:CYS53 4.6 203.2 1.0
C D:CYS45 4.7 172.9 1.0
C D:CYS42 4.8 160.3 1.0
N D:ARG46 5.0 165.6 1.0

Zinc binding site 9 out of 10 in 8q7h

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Zinc binding site 9 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:135.7
occ:1.00
 OD2 D:ASP97 2.0 115.5 1.0
ND1 D:HIS77 2.0 110.8 1.0
SG D:CYS75 2.3 107.3 1.0
SG D:CYS94 2.3 116.3 1.0
CE1 D:HIS77 2.4 110.8 1.0
CG D:ASP97 2.7 115.5 1.0
OD1 D:ASP97 3.0 115.5 1.0
CB D:CYS75 3.2 107.3 1.0
CG D:HIS77 3.3 110.8 1.0
CB D:CYS94 3.5 116.3 1.0
NE2 D:HIS77 3.6 110.8 1.0
CB D:ASP97 3.9 115.5 1.0
CD2 D:HIS77 4.1 110.8 1.0
CB D:HIS77 4.1 110.8 1.0
O D:CYS75 4.1 107.3 1.0
N D:ASP97 4.1 115.5 1.0
CB D:LEU96 4.2 115.8 1.0
CA D:CYS75 4.4 107.3 1.0
C D:CYS75 4.4 107.3 1.0
CA D:ASP97 4.6 115.5 1.0
C D:LEU96 4.7 115.8 1.0
N D:LEU96 4.8 115.8 1.0
CA D:LEU96 4.8 115.8 1.0
N D:HIS77 4.8 110.8 1.0
CA D:CYS94 4.9 116.3 1.0
CE2 D:PHE79 4.9 137.3 1.0
CG D:LEU96 4.9 115.8 1.0

Zinc binding site 10 out of 10 in 8q7h

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Zinc binding site 10 out of 10 in the Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of CUL9-RBX1 Ubiquitin E3 Ligase Complex in Unneddylated and Neddylated Conformation - Focused Cullin Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:244.2
occ:1.00
 CB D:CYS53 1.8 203.2 1.0
ND1 D:HIS82 2.0 174.0 1.0
SG D:CYS56 2.3 222.1 1.0
SG D:CYS68 2.3 192.3 1.0
SG D:CYS53 2.3 203.2 1.0
CE1 D:HIS82 2.9 174.0 1.0
CB D:CYS68 3.0 192.3 1.0
CG D:HIS82 3.0 174.0 1.0
CA D:CYS53 3.3 203.2 1.0
CB D:HIS82 3.4 174.0 1.0
N D:CYS53 3.9 203.2 1.0
CB D:CYS56 3.9 222.1 1.0
NE2 D:HIS82 4.0 174.0 1.0
C D:CYS53 4.0 203.2 1.0
CD2 D:HIS82 4.1 174.0 1.0
O D:CYS53 4.2 203.2 1.0
CA D:CYS68 4.2 192.3 1.0
N D:CYS68 4.3 192.3 1.0
N D:CYS56 4.4 222.1 1.0
CA D:CYS56 4.8 222.1 1.0
CA D:HIS82 4.8 174.0 1.0
N D:ILE54 5.0 209.2 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 09:58:52 2024

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