Zinc in PDB 7oni: Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*

Enzymatic activity of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*

All present enzymatic activity of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*:
2.3.2.31;

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* (pdb code 7oni). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*, PDB code: 7oni:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7oni

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Zinc binding site 1 out of 7 in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:101.6
occ:1.00
NE2 H:HIS265 2.0 69.7 1.0
SG H:CYS260 2.3 90.6 1.0
SG H:CYS270 2.3 79.1 1.0
SG H:CYS257 2.3 87.8 1.0
CE1 H:HIS265 2.5 69.7 1.0
CD2 H:HIS265 3.3 69.7 1.0
CB H:CYS257 3.3 87.8 1.0
CB H:CYS270 3.3 79.1 1.0
CB H:CYS260 3.7 90.6 1.0
ND1 H:HIS265 3.8 69.7 1.0
N H:CYS260 3.8 90.6 1.0
CA H:CYS270 3.9 79.1 1.0
O H:CYS260 4.0 90.6 1.0
CG H:HIS265 4.2 69.7 1.0
CA H:CYS260 4.2 90.6 1.0
N H:CYS270 4.5 79.1 1.0
C H:CYS260 4.6 90.6 1.0
CB H:ALA244 4.6 82.7 1.0
CA H:CYS257 4.7 87.8 1.0
CB H:LYS259 4.8 87.9 1.0
C H:LYS259 4.9 87.9 1.0

Zinc binding site 2 out of 7 in 7oni

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Zinc binding site 2 out of 7 in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn502

b:311.3
occ:1.00
SG H:CYS161 2.3 269.4 1.0
SG H:CYS139 2.3 299.9 1.0
SG H:CYS164 2.3 253.4 1.0
SG H:CYS142 2.3 303.5 1.0
CB H:CYS139 2.9 299.9 1.0
CB H:CYS164 3.1 253.4 1.0
CB H:CYS142 3.2 303.5 1.0
CB H:CYS161 3.6 269.4 1.0
N H:CYS142 3.9 303.5 1.0
N H:CYS161 3.9 269.4 1.0
CA H:CYS142 4.2 303.5 1.0
CA H:CYS161 4.2 269.4 1.0
CA H:CYS164 4.2 253.4 1.0
N H:CYS164 4.2 253.4 1.0
CA H:CYS139 4.4 299.9 1.0
O H:CYS161 4.4 269.4 1.0
C H:CYS161 4.7 269.4 1.0
C H:VAL141 4.8 298.9 1.0
C H:CYS139 5.0 299.9 1.0

Zinc binding site 3 out of 7 in 7oni

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Zinc binding site 3 out of 7 in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn503

b:147.1
occ:1.00
SG H:CYS252 2.3 121.8 1.0
SG H:CYS228 2.3 117.4 1.0
SG H:CYS249 2.3 120.1 1.0
SG H:CYS233 2.3 130.2 1.0
CB H:CYS249 3.0 120.1 1.0
CB H:CYS233 3.4 130.2 1.0
CB H:CYS252 3.6 121.8 1.0
CB H:CYS228 3.7 117.4 1.0
N H:CYS252 4.0 121.8 1.0
CA H:CYS252 4.3 121.8 1.0
CA H:CYS249 4.4 120.1 1.0
CB H:MET235 4.6 126.6 1.0
CG H:MET235 4.7 126.6 1.0
CB H:ARG251 4.7 123.0 1.0
O H:CYS249 4.8 120.1 1.0
OE1 H:GLU254 4.8 113.0 1.0
CA H:CYS233 4.8 130.2 1.0
C H:CYS249 4.8 120.1 1.0
C H:ARG251 5.0 123.0 1.0
C H:CYS252 5.0 121.8 1.0
CA H:CYS228 5.0 117.4 1.0

Zinc binding site 4 out of 7 in 7oni

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Zinc binding site 4 out of 7 in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn504

b:253.5
occ:1.00
ND1 H:HIS158 2.0 250.1 1.0
SG H:CYS156 2.3 241.8 1.0
SG H:CYS188 2.3 228.4 1.0
SG H:CYS183 2.3 234.3 1.0
CE1 H:HIS158 2.9 250.1 1.0
CG H:HIS158 3.0 250.1 1.0
CB H:CYS183 3.0 234.3 1.0
CB H:CYS156 3.2 241.8 1.0
CB H:CYS188 3.3 228.4 1.0
CB H:HIS158 3.4 250.1 1.0
NE2 H:HIS158 3.9 250.1 1.0
CD2 H:HIS158 4.0 250.1 1.0
CB H:ALA185 4.2 240.6 1.0
CA H:CYS183 4.5 234.3 1.0
CA H:CYS156 4.6 241.8 1.0
CA H:HIS158 4.7 250.1 1.0
CA H:CYS188 4.7 228.4 1.0
N H:HIS158 4.8 250.1 1.0
CB H:LEU190 4.9 216.1 1.0
N H:ALA185 4.9 240.6 1.0

Zinc binding site 5 out of 7 in 7oni

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Zinc binding site 5 out of 7 in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:67.5
occ:1.00
ND1 R:HIS85 2.0 63.8 1.0
SG R:CYS50 2.3 60.3 1.0
SG R:CYS53 2.3 61.2 1.0
SG R:CYS88 2.3 69.8 1.0
CB R:CYS50 2.9 60.3 1.0
CE1 R:HIS85 2.9 63.8 1.0
CG R:HIS85 3.0 63.8 1.0
CB R:HIS85 3.4 63.8 1.0
CB R:CYS88 3.5 69.8 1.0
CB R:CYS53 3.9 61.2 1.0
NE2 R:HIS85 4.0 63.8 1.0
CD2 R:HIS85 4.0 63.8 1.0
N R:CYS53 4.1 61.2 1.0
N R:HIS85 4.3 63.8 1.0
CA R:CYS50 4.4 60.3 1.0
CA R:HIS85 4.4 63.8 1.0
CA R:CYS53 4.6 61.2 1.0
CB R:ILE52 4.6 56.6 1.0
CB R:CYS61 4.7 73.5 1.0
CA R:CYS88 4.9 69.8 1.0
C R:CYS50 5.0 60.3 1.0

Zinc binding site 6 out of 7 in 7oni

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Zinc binding site 6 out of 7 in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:111.3
occ:1.00
SG R:CYS61 2.3 73.5 1.0
SG R:CYS64 2.3 74.9 1.0
SG R:CYS73 2.3 78.7 1.0
SG R:CYS87 2.3 73.6 1.0
CB R:CYS64 3.2 74.9 1.0
CB R:CYS73 3.2 78.7 1.0
CB R:CYS61 3.5 73.5 1.0
CB R:CYS87 3.6 73.6 1.0
CA R:CYS73 4.1 78.7 1.0
N R:CYS64 4.3 74.9 1.0
CA R:CYS64 4.3 74.9 1.0
N R:CYS61 4.3 73.5 1.0
CA R:CYS61 4.4 73.5 1.0
CA R:CYS87 4.9 73.6 1.0
O R:CYS61 4.9 73.5 1.0
N R:CYS87 4.9 73.6 1.0
C R:CYS61 4.9 73.5 1.0

Zinc binding site 7 out of 7 in 7oni

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Zinc binding site 7 out of 7 in the Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Neddylated CUL5 C-Terminal Region-RBX2-ARIH2* within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn203

b:97.3
occ:1.00
ND1 R:HIS82 2.0 73.2 1.0
SG R:CYS80 2.3 83.5 1.0
SG R:CYS99 2.3 73.8 1.0
SG R:CYS102 2.3 80.2 1.0
CE1 R:HIS82 2.9 73.2 1.0
CB R:CYS80 3.1 83.5 1.0
CB R:CYS99 3.1 73.8 1.0
CG R:HIS82 3.1 73.2 1.0
CB R:HIS82 3.6 73.2 1.0
CB R:CYS102 3.8 80.2 1.0
N R:CYS102 3.8 80.2 1.0
NE2 R:HIS82 4.0 73.2 1.0
O R:CYS102 4.1 80.2 1.0
CD2 R:HIS82 4.2 73.2 1.0
CA R:CYS102 4.3 80.2 1.0
CA R:CYS80 4.4 83.5 1.0
CB R:LEU101 4.4 70.4 1.0
O R:CYS80 4.5 83.5 1.0
C R:CYS80 4.6 83.5 1.0
CA R:CYS99 4.6 73.8 1.0
C R:CYS102 4.7 80.2 1.0
C R:LEU101 4.9 70.4 1.0
CA R:HIS82 4.9 73.2 1.0
N R:HIS82 5.0 73.2 1.0
N R:LEU101 5.0 70.4 1.0

Reference:

S.P.Kostrhon, J.R.Prabu. CUL5-ARIH2 E3-E3 Ubiquitin Ligase Structure Reveals Cullin-Specific NEDD8 Activation To Be Published.
DOI: 10.1038/S41589-021-00858-8
Page generated: Fri Sep 24 17:09:14 2021

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