Zinc in PDB 8ikv: Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub

All present enzymatic activity of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub:
2.3.2.31;

The structure of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub, PDB code: 8ikv 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)	38.24 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.45, 76.426, 114.329, 90, 100.49, 90
R / Rfree (%)	19.8 / 21.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub (pdb code 8ikv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub, PDB code: 8ikv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:60.3 occ:1.00 SG C:CYS196 2.2 72.4 1.0 SG C:CYS201 2.3 62.5 1.0 SG C:CYS169 2.4 63.7 1.0 SG C:CYS166 2.5 54.9 1.0 CB C:CYS166 3.2 52.2 1.0 CB C:CYS169 3.2 67.6 1.0 CB C:CYS201 3.2 67.2 1.0 CB C:CYS196 3.3 69.4 1.0 OG1 C:THR168 3.6 67.2 1.0 N C:CYS169 3.7 67.5 1.0 CA C:CYS169 4.0 70.5 1.0 OG1 C:THR173 4.1 73.8 1.0 CA C:GLY203 4.2 58.2 1.0 N C:GLY203 4.4 61.9 1.0 CA C:CYS196 4.6 71.1 1.0 CA C:CYS166 4.6 52.6 1.0 CA C:CYS201 4.7 71.9 1.0 C C:THR168 4.8 66.6 1.0 CB C:SER198 4.8 84.5 1.0 CB C:THR168 4.9 65.7 1.0 C C:CYS169 5.0 74.0 1.0

Zinc binding site 2 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:31.1 occ:1.00 NE2 C:HIS373 2.0 25.2 1.0 SG C:CYS365 2.4 30.8 1.0 SG C:CYS377 2.4 37.2 1.0 SG C:CYS368 2.4 34.0 1.0 CE1 C:HIS373 2.8 26.0 1.0 CD2 C:HIS373 3.1 26.4 1.0 CB C:CYS365 3.2 29.1 1.0 CB C:CYS368 3.3 34.1 1.0 CB C:CYS377 3.4 39.1 1.0 N C:CYS368 3.7 35.8 1.0 CA C:CYS377 3.9 41.3 1.0 ND1 C:HIS373 4.0 26.2 1.0 NH1 C:ARG348 4.0 32.9 1.0 CA C:CYS368 4.1 34.4 1.0 O C:HOH642 4.1 30.1 1.0 CG C:HIS373 4.2 27.0 1.0 CB C:GLU367 4.4 42.1 1.0 N C:CYS377 4.5 42.9 1.0 CA C:CYS365 4.6 29.3 1.0 C C:GLU367 4.6 37.4 1.0 CA C:GLU367 4.8 38.4 1.0 N C:GLU367 4.9 36.8 1.0 C C:CYS365 5.0 29.7 1.0 C C:CYS368 5.0 33.3 1.0

Zinc binding site 3 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:38.6 occ:1.00 ND1 C:HIS257 2.2 40.5 1.0 SG C:CYS253 2.3 37.4 1.0 SG C:CYS289 2.3 42.7 1.0 SG C:CYS293 2.3 46.4 1.0 CE1 C:HIS257 3.1 40.5 1.0 CG C:HIS257 3.2 40.0 1.0 CB C:CYS289 3.2 40.9 1.0 CB C:CYS253 3.2 40.1 1.0 CB C:CYS293 3.4 46.0 1.0 CB C:HIS257 3.5 39.4 1.0 O C:HOH674 3.8 44.7 1.0 CB C:ALA291 4.1 46.0 1.0 NE2 C:HIS257 4.3 41.5 1.0 CD2 C:HIS257 4.3 40.6 1.0 N C:HIS257 4.3 37.2 1.0 CB C:SER255 4.5 41.7 1.0 CA C:HIS257 4.5 38.2 1.0 CA C:CYS289 4.7 39.8 1.0 CA C:CYS293 4.7 45.7 1.0 CA C:CYS253 4.7 41.2 1.0 N C:CYS293 4.7 46.4 1.0 N C:ALA291 4.9 44.7 1.0 CB C:PHE251 5.0 32.0 1.0

Zinc binding site 4 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn504 b:31.4 occ:1.00 NE2 C:HIS461 2.1 33.0 1.0 SG C:CYS457 2.2 31.8 1.0 SG C:CYS449 2.3 36.4 1.0 SG C:CYS446 2.4 31.5 1.0 CE1 C:HIS461 3.0 32.6 1.0 CB C:CYS457 3.1 29.2 1.0 CD2 C:HIS461 3.2 32.4 1.0 CB C:CYS449 3.2 39.1 1.0 CB C:CYS446 3.3 33.5 1.0 CA C:CYS457 3.9 30.5 1.0 N C:CYS449 4.0 40.8 1.0 ND1 C:HIS461 4.1 34.5 1.0 CA C:CYS449 4.2 40.3 1.0 CG C:HIS461 4.3 33.1 1.0 CB C:ASN448 4.3 47.6 1.0 SG C:CYS451 4.6 35.5 1.0 CA C:CYS446 4.8 35.1 1.0 C C:ASN448 4.8 43.5 1.0 ND2 C:ASN448 4.8 48.6 1.0 N C:CYS457 4.8 30.9 1.0 C C:CYS457 4.9 29.9 1.0 CA C:ASN448 4.9 44.4 1.0

Zinc binding site 5 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn505 b:41.4 occ:1.00 SG C:CYS260 2.3 37.4 1.0 SG C:CYS263 2.4 42.9 1.0 SG C:CYS238 2.4 38.4 1.0 SG C:CYS241 2.5 45.5 1.0 CB C:CYS238 3.2 38.8 1.0 CB C:CYS263 3.2 39.7 1.0 CB C:CYS260 3.3 34.1 1.0 CB C:CYS241 3.3 42.0 1.0 OG1 C:THR240 3.8 42.6 1.0 N C:CYS260 3.9 34.5 1.0 N C:CYS241 3.9 43.8 1.0 CA C:CYS260 4.1 35.2 1.0 CA C:CYS241 4.2 43.6 1.0 N C:CYS263 4.2 39.2 1.0 CA C:CYS263 4.3 39.0 1.0 O C:CYS260 4.6 35.5 1.0 CA C:CYS238 4.6 38.8 1.0 C C:CYS260 4.7 34.5 1.0 CD C:ARG245 4.8 44.5 1.0 C C:CYS241 4.9 43.6 1.0 C C:THR240 4.9 42.2 1.0 CG1 C:ILE259 5.0 33.6 1.0

Zinc binding site 6 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn506 b:32.9 occ:1.00 SG C:CYS332 2.2 30.0 1.0 SG C:CYS337 2.2 38.7 1.0 SG C:CYS360 2.3 34.1 1.0 SG C:CYS352 2.3 32.1 1.0 CB C:CYS332 3.0 28.7 1.0 CB C:CYS352 3.2 32.4 1.0 CB C:CYS337 3.2 38.9 1.0 CB C:CYS360 3.4 34.3 1.0 N C:CYS360 3.9 36.7 1.0 CA C:CYS360 4.2 34.6 1.0 CA C:CYS332 4.5 29.5 1.0 CB C:ARG334 4.5 36.6 1.0 CB C:ALA339 4.6 29.1 1.0 CA C:CYS337 4.6 38.1 1.0 CA C:CYS352 4.6 33.3 1.0 CB C:PHE362 4.8 28.8 1.0 N C:GLY338 4.8 35.7 1.0 C C:CYS360 4.8 35.3 1.0 N C:ALA339 4.8 31.6 1.0 NE C:ARG334 4.9 40.5 1.0 N C:GLY361 4.9 33.9 1.0 C C:GLY359 4.9 39.3 1.0

Zinc binding site 7 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn507 b:42.5 occ:1.00 SG C:CYS436 2.2 45.1 1.0 SG C:CYS421 2.3 50.4 1.0 SG C:CYS418 2.4 45.4 1.0 SG C:CYS441 2.4 44.8 1.0 CB C:CYS436 3.2 43.9 1.0 CB C:CYS421 3.2 50.1 1.0 CB C:CYS418 3.3 46.9 1.0 CB C:CYS441 3.3 46.1 1.0 N C:CYS421 3.7 50.6 1.0 CA C:CYS421 4.0 51.9 1.0 O C:HOH611 4.6 54.9 1.0 CA C:CYS436 4.6 45.1 1.0 N C:HIS422 4.6 56.3 1.0 C C:CYS421 4.7 52.9 1.0 CB C:LEU443 4.7 41.0 1.0 CB C:ARG420 4.7 49.1 1.0 CA C:CYS441 4.7 44.9 1.0 CA C:CYS418 4.7 46.6 1.0 C C:ARG420 4.8 50.0 1.0 N C:ARG442 4.9 47.0 1.0 N C:LEU443 4.9 43.6 1.0 CB C:GLN438 4.9 47.9 1.0

Zinc binding site 8 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn508 b:38.8 occ:1.00 NE2 C:HIS215 2.1 48.9 1.0 SG C:CYS150 2.3 42.6 1.0 SG C:CYS154 2.3 44.9 1.0 SG C:CYS212 2.4 36.1 1.0 CD2 C:HIS215 2.9 49.7 1.0 CB C:CYS150 3.1 39.9 1.0 CB C:CYS212 3.2 38.3 1.0 CB C:CYS154 3.2 47.3 1.0 CE1 C:HIS215 3.2 48.6 1.0 N C:CYS154 3.8 50.8 1.0 CG C:HIS215 4.1 50.9 1.0 CA C:CYS154 4.1 48.1 1.0 CD C:PRO153 4.2 57.2 1.0 ND1 C:HIS215 4.2 48.6 1.0 CB C:ALA214 4.4 48.3 1.0 CA C:CYS150 4.6 39.7 1.0 N C:PRO153 4.6 57.0 1.0 CA C:CYS212 4.6 39.8 1.0 CG C:GLN158 4.7 40.1 1.0 NE2 C:GLN158 4.9 39.4 1.0 C C:PRO153 4.9 53.2 1.0 N C:ALA214 5.0 48.9 1.0

Zinc binding site 9 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:34.2 occ:1.00 ND1 A:HIS257 2.1 30.5 1.0 SG A:CYS253 2.2 34.9 1.0 SG A:CYS289 2.3 32.5 1.0 SG A:CYS293 2.4 38.9 1.0 CE1 A:HIS257 3.1 30.6 1.0 CG A:HIS257 3.2 30.8 1.0 CB A:CYS289 3.2 31.7 1.0 CB A:CYS253 3.3 37.6 1.0 CB A:CYS293 3.3 40.0 1.0 CB A:HIS257 3.5 30.4 1.0 O A:HOH629 3.9 58.4 1.0 CB A:ALA291 4.2 36.4 1.0 NE2 A:HIS257 4.2 30.7 1.0 CD2 A:HIS257 4.3 30.3 1.0 N A:HIS257 4.5 31.1 1.0 CA A:CYS293 4.6 40.3 1.0 CB A:SER255 4.6 39.2 1.0 N A:CYS293 4.6 39.0 1.0 CA A:HIS257 4.6 30.3 1.0 CA A:CYS289 4.6 31.2 1.0 CA A:CYS253 4.7 38.9 1.0 CB A:PHE251 4.9 26.3 1.0 OG A:SER255 5.0 40.1 1.0

Zinc binding site 10 out of 16 in the Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Publ Depleted Phospho-Parkin(K211N,R163D) in Complex with Pub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:65.1 occ:1.00 NE2 A:HIS373 1.8 73.0 1.0 SG A:CYS377 2.3 94.8 1.0 SG A:CYS368 2.3 61.0 1.0 SG A:CYS365 2.5 57.6 1.0 CE1 A:HIS373 2.8 73.9 1.0 CD2 A:HIS373 2.8 72.7 1.0 CB A:CYS365 3.2 52.0 1.0 CB A:CYS368 3.2 60.2 1.0 CB A:CYS377 3.4 98.9 1.0 CA A:CYS377 3.7 101.1 1.0 ND1 A:HIS373 3.9 73.0 1.0 N A:CYS368 3.9 59.8 1.0 CG A:HIS373 3.9 71.9 1.0 CA A:CYS368 4.1 62.0 1.0 NH1 A:ARG348 4.2 71.7 1.0 N A:CYS377 4.3 98.6 1.0 CA A:CYS365 4.7 49.3 1.0 CB A:GLU367 4.8 64.6 1.0 C A:GLU376 4.8 98.1 1.0 C A:GLU367 4.9 59.5 1.0 C A:CYS368 5.0 63.8 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