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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

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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

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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

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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

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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: Mon Oct 28 21:54:38 2024

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