Zinc in PDB 8ikt: Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub

All present enzymatic activity of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub:
2.3.2.31;

The structure of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub, PDB code: 8ikt 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)	38.42 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.764, 82.764, 103.494, 90, 90, 120
R / Rfree (%)	21.3 / 23.6

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

Zinc binding site 1 out of 6 in the Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:62.6 occ:1.00 ND1 A:HIS257 1.9 63.0 1.0 SG A:CYS289 2.3 60.6 1.0 SG A:CYS253 2.3 63.2 1.0 SG A:CYS293 2.3 60.1 1.0 CE1 A:HIS257 2.9 63.0 1.0 CG A:HIS257 2.9 61.0 1.0 CB A:CYS289 3.2 61.5 1.0 CB A:HIS257 3.3 58.9 1.0 CB A:CYS253 3.3 63.5 1.0 CB A:CYS293 3.4 60.7 1.0 CB A:ALA291 4.0 60.2 1.0 NE2 A:HIS257 4.0 62.7 1.0 CD2 A:HIS257 4.0 61.7 1.0 N A:HIS257 4.2 60.6 1.0 CA A:HIS257 4.3 57.4 1.0 CB A:SER255 4.3 70.2 1.0 CA A:CYS293 4.6 59.5 1.0 N A:CYS293 4.6 57.4 1.0 CA A:CYS289 4.6 60.6 1.0 CA A:CYS253 4.7 64.9 1.0 CB A:PHE251 4.8 51.3 1.0 OG A:SER255 4.8 73.0 1.0 N A:ALA291 4.9 60.0 1.0 CA A:ALA291 5.0 60.1 1.0 N A:SER255 5.0 70.7 1.0

Zinc binding site 2 out of 6 in the Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:65.0 occ:1.00 NE2 A:HIS373 2.0 66.7 1.0 SG A:CYS368 2.3 60.0 1.0 SG A:CYS365 2.3 63.3 1.0 SG A:CYS377 2.3 73.3 1.0 CE1 A:HIS373 3.0 68.0 1.0 CD2 A:HIS373 3.1 67.8 1.0 CB A:CYS365 3.2 62.8 1.0 CB A:CYS368 3.3 62.0 1.0 CB A:CYS377 3.4 74.8 1.0 N A:CYS368 3.6 63.9 1.0 CA A:CYS377 3.9 77.1 1.0 NH1 A:ARG348 4.0 73.7 1.0 CA A:CYS368 4.0 61.2 1.0 ND1 A:HIS373 4.1 69.2 1.0 CG A:HIS373 4.2 69.0 1.0 CB A:GLU367 4.5 69.8 1.0 N A:CYS377 4.5 76.7 1.0 CA A:CYS365 4.6 61.1 1.0 C A:GLU367 4.6 64.7 1.0 N A:GLU367 4.8 66.2 1.0 CA A:GLU367 4.9 67.2 1.0 C A:CYS365 4.9 61.6 1.0 C A:CYS368 4.9 61.4 1.0 O A:CYS365 5.0 61.5 1.0

Zinc binding site 3 out of 6 in the Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:103.0 occ:1.00 SG A:CYS169 2.3 100.9 1.0 SG A:CYS196 2.3 92.9 1.0 SG A:CYS201 2.3 116.2 1.0 SG A:CYS166 2.3 96.9 1.0 CB A:CYS166 3.2 93.7 1.0 CB A:CYS169 3.2 97.9 1.0 CB A:CYS196 3.2 98.3 1.0 CB A:CYS201 3.3 122.2 1.0 OG1 A:THR168 3.7 100.3 1.0 N A:CYS169 3.7 98.0 1.0 CA A:CYS169 4.0 97.1 1.0 OG A:SER198 4.3 115.5 1.0 CB A:SER198 4.4 115.4 1.0 OG1 A:THR173 4.5 91.8 1.0 CA A:CYS166 4.6 89.8 1.0 CA A:CYS196 4.6 99.9 1.0 C A:CYS169 4.7 97.0 1.0 CA A:CYS201 4.7 123.8 1.0 CA A:GLY203 4.8 118.7 1.0 C A:THR168 4.8 100.8 1.0 O A:CYS166 4.8 96.8 1.0 C A:CYS166 4.9 94.1 1.0 N A:GLY203 4.9 125.7 1.0 N A:ARG170 4.9 95.4 1.0 CB A:THR168 5.0 98.7 1.0

Zinc binding site 4 out of 6 in the Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:56.2 occ:1.00 SG A:CYS263 2.3 55.8 1.0 SG A:CYS241 2.3 60.5 1.0 SG A:CYS260 2.3 54.7 1.0 SG A:CYS238 2.3 58.3 1.0 CB A:CYS238 3.2 57.0 1.0 CB A:CYS263 3.2 54.6 1.0 CB A:CYS241 3.3 58.2 1.0 CB A:CYS260 3.3 51.6 1.0 NH2 A:ARG245 3.5 77.2 1.0 OG1 A:THR240 3.8 57.2 1.0 N A:CYS241 3.9 56.1 1.0 N A:CYS263 4.1 54.8 1.0 N A:CYS260 4.1 49.3 1.0 CA A:CYS241 4.2 56.4 1.0 CA A:CYS260 4.2 49.8 1.0 CA A:CYS263 4.2 54.7 1.0 CZ A:ARG245 4.4 77.4 1.0 NE A:ARG245 4.4 75.3 1.0 O A:CYS260 4.6 50.2 1.0 C A:CYS260 4.7 49.7 1.0 CA A:CYS238 4.7 56.4 1.0 C A:CYS241 4.9 56.0 1.0

Zinc binding site 5 out of 6 in the Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:55.9 occ:1.00 SG A:CYS337 2.3 56.5 1.0 SG A:CYS360 2.3 62.6 1.0 SG A:CYS352 2.3 57.6 1.0 SG A:CYS332 2.3 50.6 1.0 CB A:CYS352 3.1 60.1 1.0 CB A:CYS337 3.3 54.5 1.0 CB A:CYS332 3.3 48.1 1.0 CB A:CYS360 3.3 65.6 1.0 N A:CYS360 3.5 71.1 1.0 CA A:CYS360 4.0 69.2 1.0 CB A:ARG334 4.4 57.0 1.0 C A:GLY359 4.6 73.9 1.0 CA A:CYS352 4.6 62.7 1.0 CB A:ALA339 4.6 43.8 1.0 CA A:CYS337 4.6 53.1 1.0 CA A:CYS332 4.7 47.4 1.0 C A:CYS360 4.7 71.3 1.0 CA A:GLY359 4.7 73.5 1.0 CB A:PHE362 4.7 63.7 1.0 N A:GLY361 4.8 68.1 1.0 N A:GLY338 4.8 50.5 1.0 O A:CYS352 4.8 69.0 1.0 N A:ALA339 4.9 46.8 1.0 N A:PHE362 4.9 64.6 1.0

Zinc binding site 6 out of 6 in the Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ternary Trans-Complex of Phospho-Parkin with Cis Act and Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:44.0 occ:1.00 NE2 A:HIS215 1.8 43.8 1.0 SG A:CYS150 2.3 44.3 1.0 SG A:CYS154 2.3 45.8 1.0 SG A:CYS212 2.3 44.0 1.0 CD2 A:HIS215 2.8 42.9 1.0 CE1 A:HIS215 2.8 43.4 1.0 CB A:CYS150 3.2 44.5 1.0 CB A:CYS212 3.2 43.0 1.0 CB A:CYS154 3.2 46.6 1.0 ND1 A:HIS215 3.8 42.2 1.0 CG A:HIS215 3.8 41.8 1.0 N A:CYS154 3.9 48.8 1.0 O A:HOH615 3.9 62.8 1.0 CA A:CYS154 4.2 49.5 1.0 CB A:ALA214 4.2 42.2 1.0 CD A:PRO153 4.2 52.2 1.0 CG A:GLN158 4.4 43.1 1.0 N A:PRO153 4.5 52.1 1.0 CA A:CYS150 4.6 44.7 1.0 NE2 A:GLN158 4.6 43.9 1.0 CA A:CYS212 4.6 42.7 1.0 O A:GLY152 4.6 55.0 1.0 C A:GLY152 4.8 52.5 1.0 N A:ALA214 4.9 44.1 1.0 CA A:ALA214 5.0 43.0 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