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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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

Go back to Zinc Binding Sites List in 7b5l
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: Wed Mar 3 16:18:56 2021

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy