Zinc in PDB 7us1: Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules

Enzymatic activity of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules

All present enzymatic activity of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules:
2.3.2.31;

Protein crystallography data

The structure of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules, PDB code: 7us1 was solved by R.Fakih, V.Sauve, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.59 / 2.48
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 83.078, 83.078, 253.816, 90, 90, 120
R / Rfree (%) 22.9 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules (pdb code 7us1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules, PDB code: 7us1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7us1

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Zinc binding site 1 out of 6 in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:75.5
occ:1.00
 ND1 A:HIS257 2.1 80.7 1.0
SG A:CYS293 2.3 69.1 1.0
SG A:CYS289 2.3 72.9 1.0
SG A:CYS253 2.3 77.0 1.0
CE1 A:HIS257 2.9 80.3 1.0
CG A:HIS257 3.1 72.4 1.0
CB A:CYS289 3.2 69.0 1.0
CB A:CYS253 3.2 74.5 1.0
CB A:CYS293 3.4 76.4 1.0
CB A:HIS257 3.6 66.5 1.0
NE2 A:HIS257 3.9 80.0 1.0
CD2 A:HIS257 4.0 75.0 1.0
CB A:ALA291 4.2 71.3 1.0
N A:HIS257 4.5 73.6 1.0
N A:CYS293 4.5 80.5 1.0
CA A:CYS293 4.6 79.5 1.0
CA A:HIS257 4.7 71.5 1.0
CA A:CYS289 4.7 66.4 1.0
CA A:CYS253 4.7 79.0 1.0
CB A:PHE251 4.9 66.3 1.0
N A:ALA291 4.9 69.5 1.0

Zinc binding site 2 out of 6 in 7us1

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Zinc binding site 2 out of 6 in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:137.2
occ:1.00
 NE2 A:HIS373 2.1 135.5 1.0
SG A:CYS368 2.3 139.8 1.0
SG A:CYS377 2.3 167.2 1.0
SG A:CYS365 2.3 134.8 1.0
CB A:CYS365 3.0 120.4 1.0
CE1 A:HIS373 3.0 134.1 1.0
CD2 A:HIS373 3.1 130.5 1.0
CB A:CYS368 3.4 125.4 1.0
CB A:CYS377 3.5 161.4 1.0
N A:CYS368 3.6 116.9 1.0
CA A:CYS377 3.8 160.4 1.0
ND1 A:HIS373 4.1 131.2 1.0
O A:CYS377 4.1 156.5 1.0
O A:HOH625 4.1 98.6 1.0
CA A:CYS368 4.1 122.4 1.0
CG A:HIS373 4.2 130.1 1.0
CB A:ASP367 4.4 121.6 1.0
CA A:CYS365 4.4 115.1 1.0
C A:CYS377 4.5 159.7 1.0
C A:ASP367 4.7 120.1 1.0
N A:ASP367 4.7 119.1 1.0
C A:CYS365 4.8 109.2 1.0
CA A:ASP367 4.8 121.1 1.0
O A:HOH602 4.9 115.5 1.0
O A:ALA371 5.0 129.2 1.0

Zinc binding site 3 out of 6 in 7us1

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Zinc binding site 3 out of 6 in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:77.8
occ:1.00
 SG A:CYS169 2.3 83.2 1.0
SG A:CYS166 2.3 74.0 1.0
SG A:CYS196 2.3 76.7 1.0
SG A:CYS201 2.3 84.3 1.0
CB A:CYS166 3.0 74.8 1.0
CB A:CYS169 3.2 84.8 1.0
CB A:CYS196 3.3 81.4 1.0
CB A:CYS201 3.4 89.6 1.0
OG1 A:THR168 3.6 94.3 1.0
N A:CYS169 3.7 83.6 1.0
CA A:CYS169 4.1 85.6 1.0
OG1 A:THR173 4.3 72.4 1.0
CA A:CYS166 4.5 74.7 1.0
N A:GLY203 4.5 90.0 1.0
CA A:GLY203 4.6 81.1 1.0
CA A:CYS196 4.7 80.2 1.0
CA A:CYS201 4.7 100.8 1.0
O A:CYS201 4.7 91.8 1.0
C A:CYS169 4.8 81.2 1.0
C A:CYS201 4.9 95.0 1.0
C A:THR168 4.9 85.0 1.0
CB A:THR168 4.9 85.3 1.0
CB A:SER198 4.9 95.1 1.0

Zinc binding site 4 out of 6 in 7us1

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Zinc binding site 4 out of 6 in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:89.7
occ:1.00
 SG A:CYS260 2.3 80.3 1.0
SG A:CYS263 2.3 81.0 1.0
SG A:CYS241 2.3 93.8 1.0
SG A:CYS238 2.3 93.5 1.0
CB A:CYS263 3.1 70.1 1.0
CB A:CYS238 3.1 90.6 1.0
CB A:CYS241 3.2 91.6 1.0
N A:CYS241 3.5 95.8 1.0
CB A:CYS260 3.7 76.1 1.0
CA A:CYS241 3.9 96.7 1.0
N A:CYS260 4.1 72.2 1.0
N A:CYS263 4.3 72.8 1.0
CA A:CYS263 4.3 73.1 1.0
CB A:ALA240 4.3 72.8 1.0
CA A:CYS260 4.5 72.8 1.0
C A:ALA240 4.6 95.3 1.0
CA A:CYS238 4.6 87.0 1.0
C A:CYS241 4.8 103.9 1.0
CA A:ALA240 4.8 88.3 1.0
N A:ALA240 4.8 86.3 1.0
CG1 A:ILE259 4.9 71.8 1.0
O A:CYS260 4.9 67.4 1.0
N A:THR242 5.0 110.4 1.0
C A:CYS260 5.0 73.5 1.0

Zinc binding site 5 out of 6 in 7us1

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Zinc binding site 5 out of 6 in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:80.4
occ:1.00
 SG A:CYS337 2.3 90.2 1.0
SG A:CYS360 2.3 87.6 1.0
SG A:CYS332 2.3 90.4 1.0
SG A:CYS352 2.3 100.1 1.0
CB A:CYS360 3.3 91.7 1.0
CB A:CYS332 3.3 80.8 1.0
CB A:CYS337 3.3 82.3 1.0
CB A:CYS352 3.3 95.6 1.0
N A:CYS360 3.6 101.9 1.0
CA A:CYS360 4.0 95.1 1.0
CB A:ALA339 4.4 80.5 1.0
C A:CYS360 4.6 94.9 1.0
CA A:CYS332 4.7 76.2 1.0
CA A:CYS337 4.7 87.1 1.0
C A:GLY359 4.7 104.7 1.0
N A:GLY361 4.8 94.3 1.0
CB A:ARG334 4.8 87.9 1.0
CA A:CYS352 4.8 104.0 1.0
CB A:PHE362 4.8 89.1 1.0
N A:ALA339 4.8 81.2 1.0
N A:PHE362 4.9 90.9 1.0
CA A:GLY359 5.0 110.8 1.0

Zinc binding site 6 out of 6 in 7us1

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Zinc binding site 6 out of 6 in the Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Parkin (R0RB) Bound to Two Phospho-Ubiquitin Molecules within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:52.6
occ:1.00
 NE2 A:HIS215 2.1 55.9 1.0
SG A:CYS154 2.3 48.2 1.0
SG A:CYS150 2.3 49.1 1.0
SG A:CYS212 2.3 46.8 1.0
CD2 A:HIS215 2.8 53.5 1.0
CB A:CYS150 3.0 53.7 1.0
CE1 A:HIS215 3.2 50.6 1.0
CB A:CYS154 3.2 49.5 1.0
CB A:CYS212 3.3 41.6 1.0
CG A:HIS215 4.0 47.4 1.0
N A:CYS154 4.1 54.1 1.0
ND1 A:HIS215 4.2 44.3 1.0
CA A:CYS154 4.3 53.8 1.0
CD A:PRO153 4.3 55.5 1.0
CG A:GLN158 4.4 49.9 1.0
CA A:CYS150 4.5 56.4 1.0
CB A:ALA214 4.5 54.4 1.0
N A:PRO153 4.7 57.6 1.0
CA A:CYS212 4.7 56.7 1.0
O A:GLY152 4.7 64.1 1.0
NE2 A:GLN158 4.8 57.8 1.0
CB A:GLN158 4.8 55.1 1.0
C A:GLY152 4.9 62.4 1.0
CG A:PRO153 5.0 58.0 1.0

Reference:

R.Fakih, V.Sauve, K.Gehring. Structure of the Second Phosphoubiquitin-Binding Site in Parkin. J.Biol.Chem. V. 298 02114 2022.
ISSN: ESSN 1083-351X
PubMed: 35690145
DOI: 10.1016/J.JBC.2022.102114
Page generated: Sat Apr 8 04:26:56 2023

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