Atomistry » Zinc » PDB 6gcy-6go2 » 6glc
Atomistry »
  Zinc »
    PDB 6gcy-6go2 »
      6glc »

Zinc in PDB 6glc: Structure of Phospho-Parkin Bound to Phospho-Ubiquitin

Enzymatic activity of Structure of Phospho-Parkin Bound to Phospho-Ubiquitin

All present enzymatic activity of Structure of Phospho-Parkin Bound to Phospho-Ubiquitin:
2.3.2.31;

Protein crystallography data

The structure of Structure of Phospho-Parkin Bound to Phospho-Ubiquitin, PDB code: 6glc was solved by C.Gladkova, S.L.Maslen, J.M.Skehel, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.79 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.931, 83.931, 105.119, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 20.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Phospho-Parkin Bound to Phospho-Ubiquitin (pdb code 6glc). 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 Phospho-Parkin Bound to Phospho-Ubiquitin, PDB code: 6glc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6glc

Go back to Zinc Binding Sites List in 6glc
Zinc binding site 1 out of 6 in the Structure of Phospho-Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

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

b:38.1
occ:1.00
 ND1 A:HIS257 2.2 35.8 1.0
SG A:CYS293 2.3 40.6 1.0
SG A:CYS253 2.3 35.6 1.0
SG A:CYS289 2.3 33.9 1.0
CE1 A:HIS257 3.1 39.3 1.0
CB A:CYS289 3.2 33.6 1.0
CB A:CYS253 3.2 38.9 1.0
CG A:HIS257 3.2 31.4 1.0
CB A:CYS293 3.4 45.0 1.0
CB A:HIS257 3.5 29.7 1.0
O A:HOH632 4.1 50.5 1.0
CB A:ALA291 4.1 37.4 1.0
NE2 A:HIS257 4.2 36.2 1.0
CD2 A:HIS257 4.3 40.3 1.0
N A:HIS257 4.4 36.5 1.0
N A:CYS293 4.6 46.5 1.0
CA A:HIS257 4.6 32.2 1.0
CA A:CYS293 4.6 46.9 1.0
CA A:CYS289 4.6 31.9 1.0
CB A:SER255 4.6 42.1 1.0
CA A:CYS253 4.6 39.4 1.0
CB A:PHE251 4.8 29.9 1.0
N A:ALA291 4.9 33.8 1.0

Zinc binding site 2 out of 6 in 6glc

Go back to Zinc Binding Sites List in 6glc
Zinc binding site 2 out of 6 in the Structure of Phospho-Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

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

b:41.5
occ:1.00
 NE2 A:HIS373 2.0 41.5 1.0
SG A:CYS368 2.2 37.5 1.0
SG A:CYS365 2.4 39.5 1.0
SG A:CYS377 2.4 45.1 1.0
CE1 A:HIS373 2.9 43.2 1.0
CD2 A:HIS373 3.0 41.3 1.0
CB A:CYS365 3.1 38.0 1.0
CB A:CYS368 3.2 36.8 1.0
CB A:CYS377 3.4 49.6 1.0
N A:CYS368 3.6 35.8 1.0
O A:HOH657 3.8 49.6 1.0
CA A:CYS377 3.9 53.2 1.0
CA A:CYS368 4.0 39.8 1.0
ND1 A:HIS373 4.1 44.6 1.0
CG A:HIS373 4.1 43.0 1.0
NH1 A:ARG348 4.2 43.3 1.0
O A:HOH708 4.3 55.8 1.0
CA A:CYS365 4.5 41.7 1.0
N A:CYS377 4.6 54.9 1.0
CB A:GLU367 4.6 41.6 1.0
C A:GLU367 4.7 37.3 1.0
C A:CYS368 4.9 48.9 1.0
C A:CYS365 4.9 40.9 1.0
N A:GLU367 5.0 37.0 1.0

Zinc binding site 3 out of 6 in 6glc

Go back to Zinc Binding Sites List in 6glc
Zinc binding site 3 out of 6 in the Structure of Phospho-Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

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

b:59.8
occ:1.00
 SG A:CYS196 2.1 49.1 1.0
SG A:CYS169 2.3 60.4 1.0
SG A:CYS166 2.4 58.7 1.0
SG A:CYS201 2.5 59.5 1.0
CB A:CYS169 2.9 59.8 1.0
CB A:CYS166 3.0 57.2 1.0
CB A:CYS201 3.1 61.6 1.0
CB A:CYS196 3.2 55.8 1.0
N A:CYS169 3.6 61.0 1.0
OG1 A:THR168 3.8 72.2 1.0
CA A:CYS169 3.8 58.2 1.0
OG A:SER198 4.3 89.1 1.0
CA A:CYS166 4.5 48.9 1.0
CB A:SER198 4.5 82.4 1.0
CA A:CYS196 4.6 62.9 1.0
CA A:CYS201 4.6 68.3 1.0
C A:CYS169 4.6 65.1 1.0
N A:GLY203 4.7 74.0 1.0
OG1 A:THR173 4.7 56.0 1.0
CA A:GLY203 4.7 68.6 1.0
C A:THR168 4.7 65.2 1.0
N A:ARG170 4.9 56.2 1.0

Zinc binding site 4 out of 6 in 6glc

Go back to Zinc Binding Sites List in 6glc
Zinc binding site 4 out of 6 in the Structure of Phospho-Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

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

b:31.0
occ:1.00
 SG A:CYS241 2.3 32.5 1.0
SG A:CYS260 2.4 29.6 1.0
SG A:CYS263 2.4 30.7 1.0
SG A:CYS238 2.4 28.6 1.0
CB A:CYS238 3.1 26.1 1.0
CB A:CYS241 3.2 34.6 1.0
CB A:CYS263 3.3 24.6 1.0
CB A:CYS260 3.5 24.3 1.0
N A:CYS241 3.7 31.8 1.0
NH2 A:ARG245 3.8 58.0 1.0
OG1 A:THR240 3.9 30.7 1.0
N A:CYS260 4.0 28.0 1.0
CA A:CYS241 4.0 36.0 1.0
N A:CYS263 4.2 28.9 1.0
CA A:CYS260 4.3 25.7 1.0
CA A:CYS263 4.4 28.4 1.0
CA A:CYS238 4.6 28.2 1.0
CZ A:ARG245 4.8 49.5 1.0
NE A:ARG245 4.8 59.3 1.0
C A:THR240 4.8 36.2 1.0
C A:CYS241 4.8 38.2 1.0
C A:CYS260 4.8 26.2 1.0
O A:CYS260 4.8 27.9 1.0
CG1 A:ILE259 5.0 23.6 1.0
N A:THR242 5.0 32.3 1.0

Zinc binding site 5 out of 6 in 6glc

Go back to Zinc Binding Sites List in 6glc
Zinc binding site 5 out of 6 in the Structure of Phospho-Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

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

b:35.4
occ:1.00
 SG A:CYS360 2.3 40.5 1.0
SG A:CYS337 2.3 35.6 1.0
SG A:CYS332 2.3 33.1 1.0
SG A:CYS352 2.4 39.2 1.0
CB A:CYS352 3.1 37.0 1.0
CB A:CYS332 3.1 32.4 1.0
CB A:CYS337 3.2 37.3 1.0
CB A:CYS360 3.3 49.4 1.0
N A:CYS360 3.7 48.4 1.0
CA A:CYS360 4.1 43.7 1.0
CB A:ARG334 4.3 39.2 1.0
CA A:CYS352 4.5 37.4 1.0
CA A:CYS337 4.6 37.7 1.0
CB A:ALA339 4.6 28.1 1.0
CA A:CYS332 4.6 27.8 1.0
O A:HOH717 4.7 55.3 1.0
C A:GLY359 4.7 55.4 1.0
CB A:PHE362 4.8 36.4 1.0
C A:CYS360 4.8 48.7 1.0
N A:GLY338 4.8 29.9 1.0
CA A:GLY359 4.9 49.8 1.0
N A:ALA339 4.9 29.4 1.0
N A:GLY361 4.9 44.0 1.0
O A:CYS352 5.0 53.9 1.0

Zinc binding site 6 out of 6 in 6glc

Go back to Zinc Binding Sites List in 6glc
Zinc binding site 6 out of 6 in the Structure of Phospho-Parkin Bound to Phospho-Ubiquitin


Mono view


Stereo pair view

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

b:28.7
occ:1.00
 NE2 A:HIS215 2.0 33.2 1.0
SG A:CYS212 2.3 29.2 1.0
SG A:CYS154 2.4 30.1 1.0
SG A:CYS150 2.4 29.3 1.0
CD2 A:HIS215 2.8 33.4 1.0
CB A:CYS150 3.1 28.5 1.0
CE1 A:HIS215 3.1 28.0 1.0
CB A:CYS212 3.2 27.1 1.0
CB A:CYS154 3.3 30.6 1.0
CG A:HIS215 4.0 36.1 1.0
N A:CYS154 4.0 30.3 1.0
ND1 A:HIS215 4.1 34.9 1.0
O A:HOH712 4.1 32.9 1.0
CA A:CYS154 4.3 31.7 1.0
CD A:PRO153 4.3 40.2 1.0
CG A:GLN158 4.4 30.7 1.0
CB A:ALA214 4.5 32.2 1.0
CA A:CYS150 4.6 22.0 1.0
N A:PRO153 4.6 45.3 1.0
CA A:CYS212 4.7 23.4 1.0
O A:GLY152 4.8 51.1 1.0
NE2 A:GLN158 4.8 30.7 1.0
C A:GLY152 4.9 48.8 1.0
CG A:PRO153 4.9 40.8 1.0
CB A:GLN158 4.9 27.5 1.0
N A:ALA214 5.0 33.8 1.0

Reference:

C.Gladkova, S.L.Maslen, J.M.Skehel, D.Komander. Mechanism of Parkin Activation By PINK1. Nature V. 559 410 2018.
ISSN: ESSN 1476-4687
PubMed: 29995846
DOI: 10.1038/S41586-018-0224-X
Page generated: Thu Aug 21 14:42:18 2025

Last articles

Zn in 6Q55
Zn in 6Q30
Zn in 6Q2Y
Zn in 6Q4R
Zn in 6Q0Z
Zn in 6Q1D
Zn in 6PZQ
Zn in 6Q0W
Zn in 6Q0V
Zn in 6PZV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy