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Zinc in PDB 7b5l: Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1

Enzymatic activity of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1

All present enzymatic activity of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1:
2.3.2.23; 2.3.2.27; 2.3.2.31; 2.3.2.32; 2.7.11.22;

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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 (pdb code 7b5l). 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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1, PDB code: 7b5l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn601

b:226.6
occ:1.00
 SG H:CYS347 2.3 142.9 1.0
SG H:CYS344 2.3 142.3 1.0
SG H:CYS367 2.3 154.7 1.0
SG H:CYS362 2.3 148.4 1.0
CB H:CYS347 2.8 142.9 1.0
CB H:CYS344 3.1 142.3 1.0
CB H:CYS362 3.3 148.4 1.0
N H:CYS347 3.4 142.9 1.0
CB H:CYS367 3.4 154.7 1.0
CA H:CYS347 3.7 142.9 1.0
O H:CYS367 4.1 154.7 1.0
C H:CYS347 4.4 142.9 1.0
CA H:CYS344 4.5 142.3 1.0
N H:HIS348 4.5 133.9 1.0
C H:LYS346 4.6 141.1 1.0
CB H:LYS346 4.6 141.1 1.0
CA H:CYS367 4.7 154.7 1.0
CA H:CYS362 4.8 148.4 1.0
C H:CYS367 4.8 154.7 1.0
CB H:ASN364 4.8 145.1 1.0
C H:CYS344 4.9 142.3 1.0
N H:LYS346 4.9 141.1 1.0
CG2 H:VAL349 5.0 121.5 1.0
CA H:LYS346 5.0 141.1 1.0

Zinc binding site 2 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn602

b:270.0
occ:1.00
 NE2 H:HIS382 2.1 210.2 1.0
SG H:CYS372 2.3 178.3 1.0
SG H:CYS375 2.3 190.2 1.0
SG H:CYS389 2.3 219.1 1.0
CD2 H:HIS382 2.4 210.2 1.0
CB H:CYS389 2.6 219.1 1.0
CB H:CYS375 2.8 190.2 1.0
CB H:CYS372 3.2 178.3 1.0
N H:CYS375 3.2 190.2 1.0
CE1 H:HIS382 3.4 210.2 1.0
CA H:CYS375 3.6 190.2 1.0
CA H:CYS389 3.7 219.1 1.0
CG H:HIS382 3.7 210.2 1.0
ND1 H:HIS382 4.1 210.2 1.0
C H:VAL374 4.4 179.9 1.0
CB H:VAL374 4.4 179.9 1.0
N H:CYS389 4.4 219.1 1.0
CA H:CYS372 4.5 178.3 1.0
C H:CYS375 4.5 190.2 1.0
N H:VAL374 4.6 179.9 1.0
CA H:VAL374 4.7 179.9 1.0
N H:LEU376 4.7 175.7 1.0
C H:CYS372 4.8 178.3 1.0
O H:CYS372 4.9 178.3 1.0
C H:CYS389 4.9 219.1 1.0
CB H:HIS382 5.0 210.2 1.0

Zinc binding site 3 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn603

b:164.8
occ:1.00
 SG H:CYS297 2.3 97.1 1.0
SG H:CYS276 2.3 78.7 1.0
SG H:CYS299 2.3 104.3 1.0
SG H:CYS281 2.3 99.0 1.0
CB H:CYS281 3.0 99.0 1.0
CB H:CYS299 3.0 104.3 1.0
CB H:CYS297 3.1 97.1 1.0
CB H:CYS276 3.1 78.7 1.0
ND1 H:HIS283 4.1 89.6 1.0
N H:CYS299 4.1 104.3 1.0
CA H:CYS299 4.2 104.3 1.0
CB H:ALA278 4.3 85.2 1.0
CA H:CYS297 4.5 97.1 1.0
CA H:CYS281 4.5 99.0 1.0
CA H:CYS276 4.5 78.7 1.0
C H:CYS297 4.7 97.1 1.0
CB H:HIS283 4.8 89.6 1.0
O H:CYS297 4.8 97.1 1.0
CG H:HIS283 4.9 89.6 1.0
C H:CYS299 4.9 104.3 1.0
CB H:ARG301 5.0 87.0 1.0
CE1 H:HIS283 5.0 89.6 1.0

Zinc binding site 4 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn604

b:102.0
occ:1.00
 NE2 H:HIS312 2.0 55.4 1.0
SG H:CYS307 2.3 70.8 1.0
SG H:CYS304 2.3 69.4 1.0
SG H:CYS317 2.3 53.1 1.0
CE1 H:HIS312 2.7 55.4 1.0
CB H:CYS304 3.0 69.4 1.0
CB H:CYS307 3.1 70.8 1.0
CD2 H:HIS312 3.2 55.4 1.0
N H:CYS307 3.8 70.8 1.0
CB H:CYS317 3.9 53.1 1.0
ND1 H:HIS312 4.0 55.4 1.0
CA H:CYS307 4.0 70.8 1.0
CG H:HIS312 4.2 55.4 1.0
CA H:CYS304 4.4 69.4 1.0
CA H:CYS317 4.5 53.1 1.0
O H:CYS304 4.6 69.4 1.0
N H:GLY308 4.6 69.8 1.0
C H:CYS304 4.8 69.4 1.0
C H:CYS307 4.8 70.8 1.0

Zinc binding site 5 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn605

b:238.5
occ:1.00
 SG H:CYS208 2.3 151.8 1.0
SG H:CYS189 2.3 167.1 1.0
SG H:CYS211 2.3 137.6 1.0
SG H:CYS186 2.3 164.9 1.0
CB H:CYS186 3.1 164.9 1.0
CB H:CYS189 3.2 167.1 1.0
CB H:CYS211 3.2 137.6 1.0
N H:CYS189 3.3 167.1 1.0
CA H:CYS189 3.8 167.1 1.0
CB H:CYS208 3.8 151.8 1.0
CB H:ILE188 4.1 148.7 1.0
C H:ILE188 4.3 148.7 1.0
CA H:CYS211 4.3 137.6 1.0
N H:CYS211 4.4 137.6 1.0
N H:CYS208 4.5 151.8 1.0
N H:ILE188 4.6 148.7 1.0
CA H:ILE188 4.6 148.7 1.0
CA H:CYS186 4.6 164.9 1.0
CA H:CYS208 4.7 151.8 1.0
C H:CYS189 4.7 167.1 1.0
CG2 H:ILE188 4.7 148.7 1.0
N H:TYR190 4.9 161.2 1.0

Zinc binding site 6 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn606

b:204.4
occ:1.00
 ND1 H:HIS205 2.0 144.5 1.0
SG H:CYS231 2.3 109.7 1.0
SG H:CYS203 2.3 157.4 1.0
SG H:CYS236 2.3 123.7 1.0
CE1 H:HIS205 2.6 144.5 1.0
CB H:CYS231 2.9 109.7 1.0
CG H:HIS205 3.2 144.5 1.0
CB H:CYS236 3.3 123.7 1.0
CB H:CYS203 3.6 157.4 1.0
NE2 H:HIS205 3.8 144.5 1.0
CB H:HIS205 3.9 144.5 1.0
CD2 H:HIS205 4.1 144.5 1.0
CA H:CYS231 4.4 109.7 1.0
N H:HIS205 4.7 144.5 1.0
CA H:CYS236 4.7 123.7 1.0
CA H:CYS203 4.9 157.4 1.0
CA H:HIS205 4.9 144.5 1.0
CB H:ALA233 5.0 115.9 1.0

Zinc binding site 7 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:53.2
occ:1.00
 ND1 R:HIS80 2.1 42.2 1.0
SG R:CYS42 2.3 41.3 1.0
SG R:CYS45 2.3 47.2 1.0
SG R:CYS83 2.3 51.4 1.0
CG R:HIS80 3.0 42.2 1.0
CE1 R:HIS80 3.1 42.2 1.0
CB R:HIS80 3.2 42.2 1.0
CB R:CYS42 3.2 41.3 1.0
CB R:CYS83 3.6 51.4 1.0
CB R:CYS45 3.7 47.2 1.0
N R:CYS45 4.2 47.2 1.0
CD2 R:HIS80 4.2 42.2 1.0
N R:HIS80 4.2 42.2 1.0
NE2 R:HIS80 4.2 42.2 1.0
CB R:CYS53 4.2 59.1 1.0
CA R:HIS80 4.3 42.2 1.0
CA R:CYS45 4.5 47.2 1.0
CA R:CYS53 4.5 59.1 1.0
CA R:CYS42 4.6 41.3 1.0
O R:CYS42 4.8 41.3 1.0
CB R:ILE44 4.9 34.7 1.0
C R:CYS42 4.9 41.3 1.0
CA R:CYS83 5.0 51.4 1.0

Zinc binding site 8 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:90.7
occ:1.00
 OD2 R:ASP97 2.0 69.0 1.0
ND1 R:HIS77 2.0 61.6 1.0
SG R:CYS75 2.3 72.6 1.0
SG R:CYS94 2.3 63.5 1.0
CG R:ASP97 2.6 69.0 1.0
OD1 R:ASP97 2.7 69.0 1.0
CE1 R:HIS77 2.9 61.6 1.0
CG R:HIS77 3.1 61.6 1.0
CB R:CYS94 3.5 63.5 1.0
CB R:HIS77 3.6 61.6 1.0
CB R:CYS75 3.6 72.6 1.0
NE2 R:HIS77 4.0 61.6 1.0
CB R:ASP97 4.1 69.0 1.0
CD2 R:HIS77 4.2 61.6 1.0
CA R:CYS75 4.8 72.6 1.0
N R:ASP97 4.8 69.0 1.0
CA R:CYS94 4.8 63.5 1.0
O R:CYS94 4.8 63.5 1.0
CA R:HIS77 4.8 61.6 1.0
N R:HIS77 4.9 61.6 1.0
O R:CYS75 4.9 72.6 1.0
O R:ASP97 4.9 69.0 1.0
CE3 R:TRP101 5.0 59.0 1.0
CZ3 R:TRP101 5.0 59.0 1.0
C R:CYS94 5.0 63.5 1.0
C R:CYS75 5.0 72.6 1.0

Zinc binding site 9 out of 9 in 7b5l

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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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1


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-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-P27- UBE2L3~Ub~ARIH1. Transition State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn203

b:87.5
occ:1.00
 ND1 R:HIS82 2.0 58.5 1.0
SG R:CYS53 2.3 59.1 1.0
SG R:CYS68 2.3 64.0 1.0
SG R:CYS56 2.3 64.6 1.0
CE1 R:HIS82 2.8 58.5 1.0
CG R:HIS82 3.2 58.5 1.0
CB R:CYS56 3.2 64.6 1.0
CB R:CYS68 3.3 64.0 1.0
CB R:CYS53 3.4 59.1 1.0
CB R:HIS82 3.7 58.5 1.0
N R:CYS56 3.9 64.6 1.0
NE2 R:HIS82 4.0 58.5 1.0
N R:CYS53 4.1 59.1 1.0
CA R:CYS68 4.1 64.0 1.0
CD2 R:HIS82 4.2 58.5 1.0
CA R:CYS56 4.2 64.6 1.0
CA R:CYS53 4.3 59.1 1.0
N R:HIS82 4.8 58.5 1.0
CA R:HIS82 4.9 58.5 1.0
C R:CYS53 4.9 59.1 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 17:27:15 2024

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