Zinc in PDB 8ikm: Trans Complex of Phospho Parkin

All present enzymatic activity of Trans Complex of Phospho Parkin:
2.3.2.31;

The structure of Trans Complex of Phospho Parkin, PDB code: 8ikm 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)	42.60 / 1.92
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.804, 83.804, 105.033, 90, 90, 120
R / Rfree (%)	20.5 / 23.3

The binding sites of Zinc atom in the Trans Complex of Phospho Parkin (pdb code 8ikm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Trans Complex of Phospho Parkin, PDB code: 8ikm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Trans Complex of Phospho Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Trans Complex of Phospho Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:40.3 occ:1.00 NE2 A:HIS215 2.0 39.6 1.0 SG A:CYS150 2.3 39.3 1.0 SG A:CYS212 2.3 39.1 1.0 SG A:CYS154 2.3 42.6 1.0 CD2 A:HIS215 2.8 42.4 1.0 CB A:CYS150 3.1 35.7 1.0 CE1 A:HIS215 3.1 42.2 1.0 CB A:CYS212 3.2 38.4 1.0 CB A:CYS154 3.3 40.1 1.0 CG A:HIS215 4.0 42.6 1.0 O A:HOH661 4.0 39.7 1.0 ND1 A:HIS215 4.1 43.3 1.0 N A:CYS154 4.1 42.4 1.0 CD A:PRO153 4.2 54.1 1.0 CA A:CYS154 4.3 42.2 1.0 CB A:ALA214 4.4 47.1 1.0 CG A:GLN158 4.4 43.0 1.0 CA A:CYS150 4.5 37.1 1.0 CA A:CYS212 4.6 37.8 1.0 N A:PRO153 4.6 53.7 1.0 O A:GLY152 4.8 60.3 1.0 NE2 A:GLN158 4.8 44.6 1.0 C A:GLY152 4.9 52.3 1.0 CB A:GLN158 4.9 42.6 1.0 N A:ALA214 4.9 44.4 1.0

Zinc binding site 2 out of 6 in the Trans Complex of Phospho Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Trans Complex of Phospho Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:115.8 occ:1.00 SG A:CYS169 2.2 103.4 1.0 SG A:CYS201 2.3 103.7 1.0 SG A:CYS196 2.4 71.8 1.0 SG A:CYS166 2.5 80.2 1.0 CB A:CYS166 3.1 81.9 1.0 CB A:CYS196 3.2 86.2 1.0 CB A:CYS169 3.2 96.8 1.0 CB A:CYS201 3.4 109.2 1.0 OG1 A:THR168 3.8 90.5 1.0 N A:CYS169 3.8 93.5 1.0 CA A:CYS169 4.1 95.2 1.0 CA A:GLY203 4.2 95.6 1.0 OG1 A:THR173 4.4 77.4 1.0 N A:GLY203 4.5 101.3 1.0 CA A:CYS166 4.6 81.9 1.0 CA A:CYS196 4.6 94.1 1.0 CA A:CYS201 4.7 109.4 1.0 C A:CYS169 4.8 91.2 1.0 C A:THR168 4.9 93.0 1.0 C A:CYS201 5.0 107.7 1.0

Zinc binding site 3 out of 6 in the Trans Complex of Phospho Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Trans Complex of Phospho Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:57.8 occ:1.00 SG A:CYS289 2.2 55.6 1.0 SG A:CYS253 2.3 55.3 1.0 ND1 A:HIS257 2.4 60.7 1.0 SG A:CYS293 2.5 68.6 1.0 CB A:CYS253 3.2 55.7 1.0 CB A:CYS289 3.2 59.7 1.0 CG A:HIS257 3.3 56.6 1.0 CE1 A:HIS257 3.3 60.9 1.0 CB A:CYS293 3.4 63.1 1.0 CB A:HIS257 3.5 55.5 1.0 O A:HOH638 4.2 72.8 1.0 CB A:ALA291 4.2 60.6 1.0 N A:HIS257 4.4 54.2 1.0 NE2 A:HIS257 4.4 62.4 1.0 CD2 A:HIS257 4.5 60.8 1.0 CA A:HIS257 4.6 54.8 1.0 CA A:CYS253 4.7 59.0 1.0 CA A:CYS289 4.7 55.6 1.0 CA A:CYS293 4.7 62.9 1.0 CB A:SER255 4.7 60.3 1.0 N A:CYS293 4.7 62.4 1.0 CB A:PHE251 4.8 47.7 1.0

Zinc binding site 4 out of 6 in the Trans Complex of Phospho Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Trans Complex of Phospho Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:54.7 occ:1.00 NE2 A:HIS373 2.0 53.2 1.0 SG A:CYS368 2.3 53.8 1.0 O A:HOH612 2.3 61.2 1.0 SG A:CYS377 2.3 56.6 1.0 SG A:CYS365 2.4 53.9 1.0 CE1 A:HIS373 3.0 55.8 1.0 CD2 A:HIS373 3.0 54.4 1.0 CB A:CYS365 3.1 51.9 1.0 CB A:CYS368 3.2 53.7 1.0 CB A:CYS377 3.5 63.7 1.0 N A:CYS368 3.6 52.6 1.0 O A:HOH657 3.9 68.7 1.0 CA A:CYS368 4.0 50.6 1.0 CA A:CYS377 4.0 68.7 1.0 ND1 A:HIS373 4.1 57.7 1.0 NH1 A:ARG348 4.1 68.9 1.0 CG A:HIS373 4.2 57.4 1.0 CA A:CYS365 4.5 50.5 1.0 CB A:GLU367 4.6 57.6 1.0 N A:CYS377 4.6 68.7 1.0 C A:GLU367 4.7 54.2 1.0 C A:CYS365 4.9 52.1 1.0 N A:GLU367 4.9 50.9 1.0 C A:CYS368 4.9 49.2 1.0 CA A:GLU367 4.9 52.6 1.0 O A:CYS365 5.0 48.3 1.0 N A:LYS369 5.0 48.3 1.0

Zinc binding site 5 out of 6 in the Trans Complex of Phospho Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Trans Complex of Phospho Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:50.0 occ:1.00 SG A:CYS241 2.1 55.2 1.0 SG A:CYS263 2.4 52.2 1.0 SG A:CYS260 2.4 50.8 1.0 SG A:CYS238 2.4 47.8 1.0 CB A:CYS238 3.1 47.7 1.0 CB A:CYS241 3.1 54.7 1.0 CB A:CYS263 3.3 51.5 1.0 CB A:CYS260 3.5 48.6 1.0 NH1 A:ARG245 3.6 77.3 1.0 N A:CYS241 3.7 52.1 1.0 OG1 A:THR240 3.7 55.1 1.0 CA A:CYS241 4.0 52.3 1.0 N A:CYS260 4.0 43.7 1.0 CA A:CYS260 4.3 44.7 1.0 N A:CYS263 4.4 51.8 1.0 CA A:CYS263 4.4 51.8 1.0 CA A:CYS238 4.6 48.8 1.0 C A:THR240 4.8 52.8 1.0 CB A:THR240 4.8 53.3 1.0 C A:CYS241 4.8 52.6 1.0 CZ A:ARG245 4.8 75.5 1.0 C A:CYS260 4.9 47.2 1.0 O A:CYS260 4.9 47.7 1.0 N A:THR242 4.9 53.2 1.0

Zinc binding site 6 out of 6 in the Trans Complex of Phospho Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Trans Complex of Phospho Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:51.8 occ:1.00 SG A:CYS337 2.3 52.6 1.0 SG A:CYS332 2.3 49.6 1.0 SG A:CYS360 2.3 57.1 1.0 SG A:CYS352 2.3 54.3 1.0 CB A:CYS352 3.1 59.5 1.0 CB A:CYS332 3.1 41.6 1.0 CB A:CYS337 3.2 52.9 1.0 CB A:CYS360 3.4 60.6 1.0 N A:CYS360 3.9 65.5 1.0 CA A:CYS360 4.2 65.5 1.0 CB A:ALA339 4.5 40.0 1.0 CB A:ARG334 4.5 56.4 1.0 CA A:CYS352 4.6 57.0 1.0 CA A:CYS332 4.6 44.3 1.0 CA A:CYS337 4.6 49.8 1.0 N A:GLY338 4.7 41.1 1.0 N A:ALA339 4.8 42.9 1.0 C A:GLY359 4.9 67.4 1.0 CB A:PHE362 4.9 56.7 1.0 C A:CYS360 4.9 68.4 1.0

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