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Zinc in PDB 7b5m: Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2

Enzymatic activity of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2

All present enzymatic activity of Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2:
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: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2 (pdb code 7b5m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2, PDB code: 7b5m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7b5m

Go back to Zinc Binding Sites List in 7b5m
Zinc binding site 1 out of 5 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2


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: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn601

b:234.1
occ:1.00
 SG H:CYS367 2.3 193.3 1.0
SG H:CYS362 2.3 183.1 1.0
SG H:CYS347 2.3 184.8 1.0
SG H:CYS344 2.3 187.9 1.0
CB H:CYS367 3.1 193.3 1.0
CB H:CYS362 3.2 183.1 1.0
CB H:CYS344 3.3 187.9 1.0
N H:CYS347 3.4 184.8 1.0
CB H:CYS347 3.7 184.8 1.0
ND2 H:ASN364 3.9 179.5 1.0
CA H:CYS347 4.0 184.8 1.0
CB H:LYS346 4.1 186.8 1.0
O H:CYS347 4.1 184.8 1.0
C H:LYS346 4.4 186.8 1.0
C H:CYS347 4.4 184.8 1.0
CA H:CYS367 4.6 193.3 1.0
CE1 H:PHE371 4.6 189.6 1.0
CA H:LYS346 4.6 186.8 1.0
N H:LYS346 4.6 186.8 1.0
CA H:CYS362 4.6 183.1 1.0
CA H:CYS344 4.7 187.9 1.0
CZ H:PHE371 4.7 189.6 1.0
CG H:ASN364 4.9 179.5 1.0
O H:CYS362 5.0 183.1 1.0

Zinc binding site 2 out of 5 in 7b5m

Go back to Zinc Binding Sites List in 7b5m
Zinc binding site 2 out of 5 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2


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: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn602

b:260.2
occ:1.00
 CE1 H:HIS382 1.8 200.7 1.0
NE2 H:HIS382 2.0 200.7 1.0
SG H:CYS375 2.3 203.2 1.0
SG H:CYS372 2.3 198.4 1.0
SG H:CYS389 2.3 185.8 1.0
N H:CYS375 3.0 203.2 1.0
ND1 H:HIS382 3.2 200.7 1.0
CB H:CYS375 3.2 203.2 1.0
CA H:CYS375 3.4 203.2 1.0
CD2 H:HIS382 3.4 200.7 1.0
CB H:CYS372 3.8 198.4 1.0
C H:VAL374 3.8 200.7 1.0
CG H:HIS382 3.9 200.7 1.0
CG2 H:VAL374 4.0 200.7 1.0
CB H:CYS389 4.1 185.8 1.0
O H:VAL374 4.4 200.7 1.0
N H:VAL374 4.5 200.7 1.0
CA H:VAL374 4.5 200.7 1.0
N H:CYS389 4.6 185.8 1.0
CA H:CYS389 4.6 185.8 1.0
CB H:VAL374 4.7 200.7 1.0
CA H:CYS372 4.9 198.4 1.0
C H:CYS375 4.9 203.2 1.0
OD1 H:ASN358 4.9 205.7 1.0
N H:CYS372 5.0 198.4 1.0
CB H:PRO381 5.0 192.2 1.0

Zinc binding site 3 out of 5 in 7b5m

Go back to Zinc Binding Sites List in 7b5m
Zinc binding site 3 out of 5 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2


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: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:89.0
occ:1.00
 ND1 R:HIS80 2.0 87.7 1.0
SG R:CYS42 2.3 63.3 1.0
SG R:CYS45 2.3 71.2 1.0
SG R:CYS83 2.3 93.2 1.0
CE1 R:HIS80 2.3 87.7 1.0
CG R:HIS80 2.7 87.7 1.0
NE2 R:HIS80 3.1 87.7 1.0
CB R:CYS45 3.2 71.2 1.0
CD2 R:HIS80 3.3 87.7 1.0
CB R:CYS42 3.4 63.3 1.0
CB R:HIS80 3.6 87.7 1.0
CB R:CYS83 3.6 93.2 1.0
N R:CYS45 3.8 71.2 1.0
CA R:CYS45 4.0 71.2 1.0
CB R:CYS53 4.1 112.7 1.0
CA R:CYS53 4.3 112.7 1.0
C R:CYS45 4.7 71.2 1.0
N R:HIS80 4.8 87.7 1.0
CA R:HIS80 4.8 87.7 1.0
CB R:ILE44 4.8 62.6 1.0
CA R:CYS42 4.8 63.3 1.0
CA R:CYS83 4.9 93.2 1.0
N R:ARG46 4.9 60.1 1.0
C R:ILE44 5.0 62.6 1.0

Zinc binding site 4 out of 5 in 7b5m

Go back to Zinc Binding Sites List in 7b5m
Zinc binding site 4 out of 5 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2


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: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:202.1
occ:1.00
 OD2 R:ASP97 2.0 108.8 1.0
ND1 R:HIS77 2.0 103.7 1.0
SG R:CYS75 2.3 111.4 1.0
SG R:CYS94 2.3 97.6 1.0
CG R:ASP97 2.8 108.8 1.0
CE1 R:HIS77 2.8 103.7 1.0
OD1 R:ASP97 2.9 108.8 1.0
CG R:HIS77 3.2 103.7 1.0
CB R:CYS94 3.5 97.6 1.0
CB R:HIS77 3.7 103.7 1.0
CB R:CYS75 3.9 111.4 1.0
NE2 R:HIS77 4.0 103.7 1.0
CD2 R:HIS77 4.2 103.7 1.0
CB R:ASP97 4.2 108.8 1.0
O R:CYS75 4.3 111.4 1.0
NH1 R:ARG99 4.5 107.2 1.0
C R:CYS75 4.7 111.4 1.0
CZ3 R:TRP101 4.8 97.2 1.0
CA R:CYS94 4.8 97.6 1.0
CA R:CYS75 4.9 111.4 1.0
CA R:HIS77 5.0 103.7 1.0

Zinc binding site 5 out of 5 in 7b5m

Go back to Zinc Binding Sites List in 7b5m
Zinc binding site 5 out of 5 in the Ubiquitin Ligation to F-Box Protein Substrates By Scf-Rbr E3-E3 Super- Assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2


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: CUL1-RBX1-SKP1-SKP2-CKSHS1-P27~Ub~ARIH1. Transition State 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn203

b:193.7
occ:1.00
 ND1 R:HIS82 2.0 116.0 1.0
SG R:CYS68 2.3 134.2 1.0
SG R:CYS53 2.3 112.7 1.0
SG R:CYS56 2.3 126.1 1.0
CE1 R:HIS82 2.4 116.0 1.0
CG R:HIS82 2.7 116.0 1.0
CB R:CYS56 2.8 126.1 1.0
CB R:CYS53 3.0 112.7 1.0
NE2 R:HIS82 3.1 116.0 1.0
CD2 R:HIS82 3.3 116.0 1.0
CB R:HIS82 3.5 116.0 1.0
N R:CYS56 3.6 126.1 1.0
CB R:CYS68 3.7 134.2 1.0
N R:CYS68 3.7 134.2 1.0
CA R:CYS56 3.9 126.1 1.0
N R:CYS53 3.9 112.7 1.0
CA R:CYS68 3.9 134.2 1.0
CA R:CYS53 4.0 112.7 1.0
N R:GLU67 4.4 149.7 1.0
C R:GLU67 4.5 149.7 1.0
N R:HIS82 4.5 116.0 1.0
CA R:HIS82 4.6 116.0 1.0
C R:CYS53 4.7 112.7 1.0
C R:GLU55 4.8 122.3 1.0
N R:GLU55 5.0 122.3 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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