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Zinc in PDB 8ik6: Publ Depleted Parkin Complex with Pubiquitin

Enzymatic activity of Publ Depleted Parkin Complex with Pubiquitin

All present enzymatic activity of Publ Depleted Parkin Complex with Pubiquitin:
2.3.2.31;

Protein crystallography data

The structure of Publ Depleted Parkin Complex with Pubiquitin, PDB code: 8ik6 was solved by D.R.Lenka, A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.15 / 3.30
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 187.805, 187.805, 141.857, 90, 90, 120
R / Rfree (%) 23.4 / 27

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Publ Depleted Parkin Complex with Pubiquitin (pdb code 8ik6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Publ Depleted Parkin Complex with Pubiquitin, PDB code: 8ik6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 8ik6

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Zinc binding site 1 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:134.2
occ:1.00
 ND1 C:HIS257 2.0 132.4 1.0
SG C:CYS293 2.3 131.2 1.0
SG C:CYS253 2.3 145.8 1.0
SG C:CYS289 2.3 121.1 1.0
CE1 C:HIS257 2.9 128.8 1.0
CG C:HIS257 3.0 129.6 1.0
CB C:CYS253 3.1 145.2 1.0
CB C:CYS293 3.3 138.3 1.0
CB C:CYS289 3.4 117.5 1.0
CB C:HIS257 3.5 123.0 1.0
NE2 C:HIS257 3.9 130.0 1.0
CB C:ALA291 3.9 126.5 1.0
CD2 C:HIS257 4.0 130.4 1.0
CA C:CYS293 4.5 141.0 1.0
N C:CYS293 4.5 144.2 1.0
CA C:CYS253 4.6 147.9 1.0
N C:HIS257 4.7 135.4 1.0
CA C:HIS257 4.7 128.4 1.0
CA C:CYS289 4.7 121.8 1.0
CA C:ALA291 4.9 137.9 1.0
N C:ALA291 4.9 136.9 1.0
CB C:SER255 5.0 140.1 1.0

Zinc binding site 2 out of 14 in 8ik6

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Zinc binding site 2 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:236.3
occ:1.00
 NE2 C:HIS373 2.1 218.5 1.0
SG C:CYS368 2.3 195.3 1.0
SG C:CYS377 2.3 234.1 1.0
SG C:CYS365 2.3 239.1 1.0
CE1 C:HIS373 3.1 209.7 1.0
CD2 C:HIS373 3.1 215.5 1.0
CB C:CYS365 3.3 217.7 1.0
CB C:CYS368 3.3 200.6 1.0
CB C:CYS377 3.5 219.1 1.0
CA C:CYS377 3.6 211.1 1.0
N C:CYS368 3.9 201.1 1.0
ND1 C:HIS373 4.2 207.2 1.0
CA C:CYS368 4.2 201.1 1.0
CG C:HIS373 4.2 211.5 1.0
N C:CYS377 4.3 211.3 1.0
CB C:GLU367 4.6 216.4 1.0
CA C:CYS365 4.8 202.9 1.0
C C:CYS377 4.8 203.9 1.0
O C:GLU376 4.8 205.1 1.0
C C:GLU376 4.9 205.5 1.0
C C:CYS368 4.9 202.3 1.0
CG C:GLU367 4.9 230.0 1.0

Zinc binding site 3 out of 14 in 8ik6

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Zinc binding site 3 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:148.4
occ:1.00
 NE2 C:HIS461 2.1 152.2 1.0
SG C:CYS449 2.3 136.7 1.0
SG C:CYS446 2.3 130.2 1.0
SG C:CYS457 2.3 132.4 1.0
CE1 C:HIS461 3.0 146.5 1.0
CD2 C:HIS461 3.1 147.7 1.0
CB C:CYS449 3.1 140.5 1.0
CB C:CYS457 3.3 133.5 1.0
CB C:CYS446 3.3 137.1 1.0
N C:CYS449 3.5 132.3 1.0
CA C:CYS457 3.8 128.5 1.0
CA C:CYS449 3.9 139.6 1.0
ND1 C:HIS461 4.1 142.5 1.0
CG C:HIS461 4.1 141.7 1.0
O C:CYS457 4.5 130.1 1.0
CZ3 C:TRP453 4.5 140.5 1.0
C C:CYS457 4.6 131.2 1.0
CA C:CYS446 4.6 148.7 1.0
C C:ASN448 4.7 142.7 1.0
CB C:ASN448 4.7 164.2 1.0
OD1 C:ASN448 4.9 182.9 1.0
N C:ASN448 4.9 146.9 1.0
CA C:ASN448 5.0 150.8 1.0
N C:CYS457 5.0 119.7 1.0

Zinc binding site 4 out of 14 in 8ik6

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Zinc binding site 4 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn504

b:124.6
occ:1.00
 SG C:CYS169 2.3 116.0 1.0
SG C:CYS201 2.3 127.9 1.0
SG C:CYS196 2.3 120.7 1.0
SG C:CYS166 2.3 129.0 1.0
CB C:CYS201 2.9 123.1 1.0
CB C:CYS166 3.0 128.4 1.0
CB C:CYS169 3.0 115.7 1.0
CB C:CYS196 3.2 123.3 1.0
N C:CYS169 3.4 115.8 1.0
CA C:CYS169 3.7 115.2 1.0
CA C:CYS201 4.3 120.0 1.0
OG1 C:THR173 4.3 120.1 1.0
C C:THR168 4.4 112.0 1.0
CA C:CYS166 4.4 126.3 1.0
CB C:THR168 4.5 106.4 1.0
CA C:CYS196 4.6 127.7 1.0
CA C:THR168 4.8 108.0 1.0
C C:CYS169 4.8 115.3 1.0
CA C:GLY203 4.8 119.0 1.0
C C:CYS166 4.8 124.5 1.0
N C:THR168 4.9 111.3 1.0
CB C:SER198 4.9 124.0 1.0
O C:CYS166 4.9 121.2 1.0
N C:GLY203 4.9 113.4 1.0

Zinc binding site 5 out of 14 in 8ik6

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Zinc binding site 5 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:151.6
occ:1.00
 SG C:CYS263 2.3 129.1 1.0
SG C:CYS238 2.3 132.6 1.0
SG C:CYS241 2.3 117.6 1.0
SG C:CYS260 2.4 161.8 1.0
CB C:CYS238 3.1 134.7 1.0
CB C:CYS263 3.2 122.0 1.0
CB C:CYS241 3.3 126.9 1.0
CB C:CYS260 3.4 133.3 1.0
N C:CYS263 3.7 118.9 1.0
CA C:CYS263 4.0 120.5 1.0
CA C:CYS260 4.3 125.7 1.0
N C:CYS260 4.3 121.8 1.0
N C:CYS241 4.4 118.6 1.0
CA C:CYS241 4.4 123.8 1.0
CA C:CYS238 4.5 137.9 1.0
O C:CYS260 4.6 120.5 1.0
C C:CYS260 4.6 123.9 1.0
CB C:ASP262 4.7 132.7 1.0
C C:ASP262 4.8 124.4 1.0

Zinc binding site 6 out of 14 in 8ik6

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Zinc binding site 6 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:203.1
occ:1.00
 SG C:CYS360 2.3 188.4 1.0
SG C:CYS332 2.3 169.0 1.0
SG C:CYS352 2.3 197.0 1.0
SG C:CYS337 2.3 184.2 1.0
CB C:CYS360 3.0 192.0 1.0
CB C:CYS332 3.1 171.5 1.0
CA C:CYS360 3.3 195.4 1.0
CB C:CYS352 3.3 183.3 1.0
CB C:CYS337 3.4 170.4 1.0
N C:CYS360 3.6 191.3 1.0
CB C:ALA339 3.8 137.1 1.0
CA C:CYS332 4.3 161.0 1.0
N C:ALA339 4.4 141.0 1.0
C C:GLY359 4.4 194.1 1.0
CA C:CYS337 4.5 164.8 1.0
CA C:ALA339 4.6 146.3 1.0
O C:ALA339 4.6 154.7 1.0
CA C:CYS352 4.7 188.3 1.0
C C:CYS360 4.7 205.5 1.0
C C:CYS337 4.8 159.7 1.0
N C:GLY338 4.9 154.2 1.0
O C:CYS352 4.9 168.7 1.0
O C:GLY359 4.9 192.4 1.0
N C:CYS332 5.0 159.9 1.0

Zinc binding site 7 out of 14 in 8ik6

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Zinc binding site 7 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn507

b:202.2
occ:1.00
 SG C:CYS441 2.3 185.2 1.0
SG C:CYS418 2.3 208.4 1.0
SG C:CYS421 2.3 182.8 1.0
SG C:CYS436 2.3 188.8 1.0
N C:CYS421 2.4 169.8 1.0
CB C:CYS421 3.2 181.4 1.0
CB C:ARG420 3.2 166.4 1.0
CB C:CYS418 3.3 183.6 1.0
CB C:CYS436 3.3 190.3 1.0
CB C:CYS441 3.3 193.2 1.0
CA C:CYS421 3.3 174.2 1.0
C C:ARG420 3.4 159.7 1.0
CA C:ARG420 3.5 166.2 1.0
N C:ARG420 3.6 176.0 1.0
N C:HIS422 4.2 170.9 1.0
C C:CYS421 4.2 173.7 1.0
CG C:ARG420 4.4 173.4 1.0
CA C:CYS418 4.5 169.0 1.0
O C:ARG420 4.5 142.2 1.0
C C:CYS418 4.6 160.6 1.0
CA C:CYS436 4.6 183.9 1.0
CA C:CYS441 4.6 193.5 1.0
CD C:ARG420 4.6 185.1 1.0
CB C:LEU443 4.6 188.5 1.0
O C:CYS418 4.8 163.7 1.0
C C:PRO419 4.9 174.0 1.0
N C:PRO419 5.0 155.7 1.0

Zinc binding site 8 out of 14 in 8ik6

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Zinc binding site 8 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn508

b:134.7
occ:1.00
 NE2 C:HIS215 1.8 144.2 1.0
SG C:CYS150 2.3 112.4 1.0
SG C:CYS212 2.3 136.8 1.0
SG C:CYS154 2.4 129.2 1.0
CD2 C:HIS215 2.8 150.9 1.0
CE1 C:HIS215 2.9 141.1 1.0
CB C:CYS150 3.0 123.0 1.0
CB C:CYS212 3.4 126.8 1.0
CB C:CYS154 3.4 125.3 1.0
CG C:HIS215 3.9 149.6 1.0
CG C:GLN158 3.9 128.2 1.0
ND1 C:HIS215 3.9 149.3 1.0
CB C:ALA214 4.0 128.3 1.0
CB C:GLN158 4.2 127.3 1.0
CA C:CYS150 4.4 120.7 1.0
CA C:CYS212 4.6 130.2 1.0
CA C:CYS154 4.7 130.3 1.0
N C:CYS154 4.7 134.6 1.0
N C:ALA214 4.9 131.0 1.0
CA C:ALA214 4.9 130.6 1.0

Zinc binding site 9 out of 14 in 8ik6

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Zinc binding site 9 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:130.0
occ:1.00
 NE2 A:HIS215 1.9 139.2 1.0
SG A:CYS150 2.3 128.1 1.0
SG A:CYS154 2.3 132.5 1.0
SG A:CYS212 2.3 119.7 1.0
CD2 A:HIS215 2.9 140.0 1.0
CE1 A:HIS215 2.9 136.4 1.0
CB A:CYS150 3.1 132.3 1.0
CB A:CYS212 3.3 124.1 1.0
CB A:CYS154 3.3 138.1 1.0
ND1 A:HIS215 4.0 135.5 1.0
CG A:HIS215 4.0 140.5 1.0
N A:CYS154 4.2 145.4 1.0
CA A:CYS154 4.4 143.4 1.0
CD A:PRO153 4.5 152.2 1.0
CA A:CYS150 4.5 139.7 1.0
CG A:GLN158 4.6 131.3 1.0
CB A:ALA214 4.7 148.2 1.0
CA A:CYS212 4.7 129.4 1.0
O A:GLY152 4.7 136.4 1.0
N A:PRO153 4.8 146.4 1.0
CB A:GLN158 4.8 127.3 1.0
C A:GLY152 4.9 142.1 1.0

Zinc binding site 10 out of 14 in 8ik6

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Zinc binding site 10 out of 14 in the Publ Depleted Parkin Complex with Pubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Publ Depleted Parkin Complex with Pubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:168.4
occ:1.00
 SG A:CYS169 2.3 145.5 1.0
SG A:CYS196 2.3 157.0 1.0
SG A:CYS166 2.3 150.3 1.0
SG A:CYS201 2.4 211.2 1.0
N A:CYS169 2.9 155.3 1.0
CB A:CYS169 3.1 142.7 1.0
CB A:CYS196 3.1 168.9 1.0
CA A:GLY203 3.3 164.9 1.0
CA A:CYS169 3.3 147.8 1.0
CB A:CYS166 3.4 147.5 1.0
CB A:CYS201 3.5 189.8 1.0
N A:GLY203 3.6 169.6 1.0
OG1 A:THR168 3.7 157.4 1.0
C A:THR168 4.0 154.4 1.0
CA A:CYS196 4.4 166.5 1.0
CB A:THR168 4.4 155.0 1.0
CA A:THR168 4.4 156.0 1.0
N A:THR168 4.4 160.5 1.0
C A:GLY203 4.7 159.4 1.0
CA A:CYS201 4.7 175.8 1.0
C A:CYS201 4.7 164.8 1.0
C A:PRO202 4.7 163.5 1.0
CA A:CYS166 4.8 148.4 1.0
C A:CYS169 4.8 152.1 1.0
O A:THR168 5.0 148.4 1.0
O A:CYS201 5.0 155.7 1.0
N A:PRO202 5.0 164.9 1.0

Reference:

D.Lenka, S.Dahe, O.Antico, P.Sahoo, A.R.Prescott, M.M.K.Muqit, A.Kumar. Additional Feedforward Mechanism of Parkin Activation Via Binding of Phospho-Ubl and RING0 in Trans Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.96699.2
Page generated: Fri Aug 22 11:10:33 2025

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