Atomistry » Zinc » PDB 7auw-7b83 » 7b5l
Atomistry »
  Zinc »
    PDB 7auw-7b83 »
      7b5l »

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: Tue Oct 29 17:27:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy