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Zinc in PDB 7b5n: Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.

Enzymatic activity of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.

All present enzymatic activity of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.:
2.3.2.23; 2.3.2.27; 2.3.2.31; 2.3.2.32;

Zinc Binding Sites:

The binding sites of Zinc atom in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. (pdb code 7b5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1., PDB code: 7b5n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7b5n

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Zinc binding site 1 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn601

b:134.7
occ:1.00
 SG H:CYS347 2.3 67.8 1.0
SG H:CYS344 2.3 63.4 1.0
SG H:CYS367 2.3 65.7 1.0
SG H:CYS362 2.3 73.4 1.0
CB H:CYS347 2.9 67.8 1.0
CB H:CYS344 3.2 63.4 1.0
CB H:CYS367 3.3 65.7 1.0
N H:CYS347 3.3 67.8 1.0
CB H:CYS362 3.4 73.4 1.0
CA H:CYS347 3.7 67.8 1.0
O H:CYS367 4.1 65.7 1.0
C H:CYS347 4.4 67.8 1.0
CB H:LYS346 4.5 62.3 1.0
C H:LYS346 4.5 62.3 1.0
N H:HIS348 4.6 64.3 1.0
CA H:CYS367 4.6 65.7 1.0
CA H:CYS344 4.6 63.4 1.0
CG1 H:VAL349 4.7 51.5 1.0
CB H:ASN364 4.7 65.6 1.0
C H:CYS367 4.8 65.7 1.0
CA H:LYS346 4.8 62.3 1.0
N H:LYS346 4.8 62.3 1.0
CA H:CYS362 4.9 73.4 1.0
ND2 H:ASN364 4.9 65.6 1.0

Zinc binding site 2 out of 9 in 7b5n

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Zinc binding site 2 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn602

b:184.0
occ:1.00
 NE2 H:HIS382 2.0 107.7 1.0
SG H:CYS372 2.3 80.7 1.0
SG H:CYS389 2.3 121.8 1.0
SG H:CYS375 2.3 84.9 1.0
CB H:CYS389 2.6 121.8 1.0
CE1 H:HIS382 2.8 107.7 1.0
CB H:CYS375 2.8 84.9 1.0
CD2 H:HIS382 2.8 107.7 1.0
N H:CYS375 3.2 84.9 1.0
CB H:CYS372 3.3 80.7 1.0
CA H:CYS375 3.6 84.9 1.0
ND1 H:HIS382 3.7 107.7 1.0
CG H:HIS382 3.7 107.7 1.0
CA H:CYS389 3.8 121.8 1.0
C H:VAL374 4.4 74.8 1.0
CB H:VAL374 4.5 74.8 1.0
C H:CYS375 4.5 84.9 1.0
N H:CYS389 4.6 121.8 1.0
CA H:CYS372 4.6 80.7 1.0
N H:VAL374 4.7 74.8 1.0
N H:LEU376 4.7 74.5 1.0
CA H:VAL374 4.8 74.8 1.0
C H:CYS372 4.8 80.7 1.0
C H:CYS389 4.9 121.8 1.0
O H:CYS372 5.0 80.7 1.0

Zinc binding site 3 out of 9 in 7b5n

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Zinc binding site 3 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn603

b:114.7
occ:1.00
 SG H:CYS297 2.3 49.4 1.0
SG H:CYS276 2.3 35.6 1.0
SG H:CYS299 2.3 56.0 1.0
SG H:CYS281 2.3 42.4 1.0
CB H:CYS281 3.0 42.4 1.0
CB H:CYS276 3.0 35.6 1.0
CB H:CYS299 3.1 56.0 1.0
CB H:CYS297 4.0 49.4 1.0
O H:CYS297 4.1 49.4 1.0
N H:CYS299 4.2 56.0 1.0
CA H:CYS299 4.2 56.0 1.0
CB H:ALA278 4.3 33.8 1.0
CA H:CYS276 4.5 35.6 1.0
CA H:CYS281 4.5 42.4 1.0
ND1 H:HIS283 4.5 37.1 1.0
CB H:ARG301 4.6 43.1 1.0
C H:CYS297 4.6 49.4 1.0
CA H:CYS297 4.8 49.4 1.0
C H:CYS299 4.9 56.0 1.0

Zinc binding site 4 out of 9 in 7b5n

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Zinc binding site 4 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn604

b:109.5
occ:1.00
 NE2 H:HIS312 2.0 26.4 1.0
SG H:CYS304 2.3 29.1 1.0
SG H:CYS307 2.3 32.0 1.0
SG H:CYS317 2.3 28.9 1.0
CE1 H:HIS312 2.7 26.4 1.0
CB H:CYS304 2.9 29.1 1.0
CD2 H:HIS312 3.2 26.4 1.0
CB H:CYS307 3.2 32.0 1.0
CB H:CYS317 3.8 28.9 1.0
ND1 H:HIS312 4.0 26.4 1.0
N H:CYS307 4.0 32.0 1.0
CA H:CYS307 4.2 32.0 1.0
CG H:HIS312 4.2 26.4 1.0
CA H:CYS304 4.4 29.1 1.0
CA H:CYS317 4.4 28.9 1.0
CB H:ALA292 4.7 39.2 1.0
O H:CYS304 4.8 29.1 1.0
C H:CYS304 4.8 29.1 1.0
C H:CYS307 4.9 32.0 1.0
C H:ASN306 5.0 25.2 1.0
N H:GLY308 5.0 25.1 1.0

Zinc binding site 5 out of 9 in 7b5n

Go back to Zinc Binding Sites List in 7b5n
Zinc binding site 5 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn605

b:181.0
occ:1.00
 SG H:CYS208 2.3 77.5 1.0
SG H:CYS186 2.3 86.7 1.0
SG H:CYS189 2.3 91.8 1.0
SG H:CYS211 2.3 66.5 1.0
CB H:CYS186 3.2 86.7 1.0
N H:CYS189 3.3 91.8 1.0
CB H:CYS189 3.3 91.8 1.0
CB H:CYS211 3.4 66.5 1.0
CB H:ILE188 3.9 77.9 1.0
CA H:CYS189 3.9 91.8 1.0
CB H:CYS208 4.0 77.5 1.0
C H:ILE188 4.3 77.9 1.0
CA H:ILE188 4.4 77.9 1.0
N H:ILE188 4.4 77.9 1.0
N H:CYS211 4.4 66.5 1.0
CA H:CYS211 4.5 66.5 1.0
CG1 H:ILE188 4.5 77.9 1.0
N H:CYS208 4.6 77.5 1.0
CA H:CYS186 4.6 86.7 1.0
CA H:CYS208 4.8 77.5 1.0
C H:CYS189 4.9 91.8 1.0
CG2 H:ILE188 4.9 77.9 1.0
O H:CYS208 4.9 77.5 1.0

Zinc binding site 6 out of 9 in 7b5n

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Zinc binding site 6 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn606

b:151.7
occ:1.00
 ND1 H:HIS205 2.0 74.8 1.0
SG H:CYS236 2.3 50.9 1.0
SG H:CYS203 2.3 86.8 1.0
SG H:CYS231 2.3 37.0 1.0
CE1 H:HIS205 2.6 74.8 1.0
CB H:CYS231 3.0 37.0 1.0
CB H:CYS236 3.3 50.9 1.0
CG H:HIS205 3.3 74.8 1.0
CB H:CYS203 3.5 86.8 1.0
NE2 H:HIS205 3.9 74.8 1.0
CB H:HIS205 3.9 74.8 1.0
CD2 H:HIS205 4.2 74.8 1.0
CA H:CYS231 4.5 37.0 1.0
CB H:ILE238 4.6 46.5 1.0
CA H:CYS236 4.7 50.9 1.0
N H:HIS205 4.7 74.8 1.0
CA H:CYS203 4.8 86.8 1.0
CG1 H:ILE238 4.9 46.5 1.0
CB H:ALA233 4.9 46.3 1.0
C H:CYS231 5.0 37.0 1.0

Zinc binding site 7 out of 9 in 7b5n

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Zinc binding site 7 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:38.8
occ:1.00
 ND1 R:HIS80 2.0 49.0 1.0
SG R:CYS42 2.3 27.1 1.0
SG R:CYS45 2.3 22.2 1.0
SG R:CYS83 2.3 23.1 1.0
CE1 R:HIS80 2.8 49.0 1.0
CG R:HIS80 3.0 49.0 1.0
CB R:CYS42 3.3 27.1 1.0
CB R:HIS80 3.4 49.0 1.0
CB R:CYS83 3.7 23.1 1.0
CB R:CYS45 3.7 22.2 1.0
NE2 R:HIS80 3.9 49.0 1.0
CD2 R:HIS80 3.9 49.0 1.0
N R:HIS80 4.1 49.0 1.0
N R:CYS45 4.1 22.2 1.0
CB R:CYS53 4.3 26.9 1.0
CA R:HIS80 4.4 49.0 1.0
CA R:CYS45 4.5 22.2 1.0
CA R:CYS53 4.7 26.9 1.0
CA R:CYS42 4.7 27.1 1.0
O R:CYS42 4.8 27.1 1.0
CB R:ILE44 4.9 20.3 1.0
C R:CYS42 5.0 27.1 1.0

Zinc binding site 8 out of 9 in 7b5n

Go back to Zinc Binding Sites List in 7b5n
Zinc binding site 8 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:51.1
occ:1.00
 OD2 R:ASP97 2.0 34.6 1.0
ND1 R:HIS77 2.0 24.3 1.0
SG R:CYS75 2.3 23.8 1.0
SG R:CYS94 2.3 26.1 1.0
CG R:ASP97 2.7 34.6 1.0
OD1 R:ASP97 2.7 34.6 1.0
CE1 R:HIS77 2.9 24.3 1.0
CG R:HIS77 3.1 24.3 1.0
CB R:CYS94 3.6 26.1 1.0
CB R:HIS77 3.6 24.3 1.0
CB R:CYS75 3.7 23.8 1.0
NE2 R:HIS77 4.0 24.3 1.0
CB R:ASP97 4.1 34.6 1.0
CD2 R:HIS77 4.2 24.3 1.0
N R:ASP97 4.8 34.6 1.0
CA R:CYS94 4.9 26.1 1.0
CA R:CYS75 4.9 23.8 1.0
CA R:HIS77 4.9 24.3 1.0
O R:ASP97 4.9 34.6 1.0
O R:CYS75 5.0 23.8 1.0

Zinc binding site 9 out of 9 in 7b5n

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Zinc binding site 9 out of 9 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn203

b:43.4
occ:1.00
 ND1 R:HIS82 2.0 25.8 1.0
SG R:CYS53 2.3 26.9 1.0
SG R:CYS68 2.3 28.2 1.0
SG R:CYS56 2.3 34.8 1.0
CE1 R:HIS82 2.7 25.8 1.0
CB R:CYS56 3.1 34.8 1.0
CG R:HIS82 3.3 25.8 1.0
CB R:CYS53 3.5 26.9 1.0
CB R:CYS68 3.6 28.2 1.0
CB R:HIS82 3.9 25.8 1.0
NE2 R:HIS82 3.9 25.8 1.0
N R:CYS56 4.0 34.8 1.0
OE1 R:GLU55 4.1 29.7 1.0
CA R:CYS56 4.2 34.8 1.0
CD2 R:HIS82 4.2 25.8 1.0
N R:CYS53 4.2 26.9 1.0
CA R:CYS53 4.4 26.9 1.0
CA R:CYS68 4.5 28.2 1.0

Reference:

D.Horn-Ghetko, D.T.Krist, J.R.Prabu, B.Kheewong, M.M.P.C.Mulder, D.C.Scott, M.Klugel, H.Ovaa, G.Kleiger, B.Schulman. Ubiquitin Ligation to F-Box Protein Targets By Scf-Rbr E3-E3 Super-Assembly Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03197-9
Page generated: Tue Oct 29 17:27:14 2024

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