Zinc in PDB 4zyn: Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)

The structure of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130), PDB code: 4zyn was solved by A.Lilov, V.Sauve, J.F.Trempe, D.Rodionov, J.Wang, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.62 / 2.54
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.105, 114.105, 186.399, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.5

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) (pdb code 4zyn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130), PDB code: 4zyn:
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 Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:47.8 occ:1.00 NE2 A:HIS215 2.1 43.1 1.0 SG A:CYS212 2.3 40.2 1.0 SG A:CYS154 2.4 45.6 1.0 SG A:CYS150 2.4 39.8 1.0 CD2 A:HIS215 2.9 45.2 1.0 CB A:CYS150 3.1 43.8 1.0 CE1 A:HIS215 3.1 43.2 1.0 CB A:CYS212 3.2 41.9 1.0 CB A:CYS154 3.3 45.9 1.0 CG A:HIS215 4.0 46.1 1.0 ND1 A:HIS215 4.1 44.0 1.0 N A:CYS154 4.1 45.8 1.0 CB A:ALA214 4.2 51.8 1.0 CD A:PRO153 4.3 45.0 1.0 CA A:CYS154 4.3 45.0 1.0 CG A:GLN158 4.4 41.1 1.0 O A:GLY152 4.5 46.5 1.0 CA A:CYS150 4.6 43.8 1.0 CA A:CYS212 4.6 42.0 1.0 N A:PRO153 4.7 45.5 1.0 C A:GLY152 4.7 45.6 1.0 NE2 A:GLN158 4.8 41.2 1.0 N A:ALA214 4.9 51.2 1.0 CB A:GLN158 5.0 40.6 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:81.3 occ:1.00 SG A:CYS169 2.0 91.9 1.0 SG A:CYS196 2.2 83.4 1.0 SG A:CYS201 2.3 84.9 1.0 SG A:CYS166 2.4 73.1 1.0 CB A:CYS166 3.1 68.8 1.0 CB A:CYS169 3.2 90.9 1.0 CB A:CYS196 3.3 86.5 1.0 CB A:CYS201 3.3 92.2 1.0 CB A:SER198 3.8 0.7 1.0 OG A:SER198 3.9 0.7 1.0 N A:CYS169 4.1 88.2 1.0 CA A:CYS169 4.2 88.8 1.0 CA A:CYS166 4.6 66.1 1.0 CA A:CYS196 4.7 87.2 1.0 CA A:CYS201 4.7 95.0 1.0 OG1 A:THR173 4.8 83.3 1.0 N A:SER198 4.8 0.0 1.0 C A:CYS169 4.9 87.8 1.0 CA A:SER198 4.9 0.6 1.0 N A:GLY203 4.9 87.2 1.0 O A:CYS166 4.9 67.7 1.0 O A:GLY203 5.0 79.5 1.0 CA A:GLY203 5.0 83.1 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:55.8 occ:1.00 SG A:CYS241 2.0 59.8 1.0 SG A:CYS260 2.2 53.2 1.0 SG A:CYS263 2.4 52.2 1.0 SG A:CYS238 2.4 52.0 1.0 CB A:CYS238 3.1 53.8 1.0 CB A:CYS260 3.3 48.6 1.0 CB A:CYS241 3.3 55.4 1.0 CB A:CYS263 3.4 55.7 1.0 N A:CYS241 3.7 54.6 1.0 N A:CYS260 4.0 44.0 1.0 CA A:CYS241 4.1 55.0 1.0 CA A:CYS260 4.2 47.2 1.0 CB A:ALA240 4.3 59.1 1.0 N A:CYS263 4.3 55.8 1.0 CA A:CYS263 4.4 56.0 1.0 CA A:CYS238 4.6 54.5 1.0 C A:ALA240 4.7 57.4 1.0 O A:CYS260 4.7 46.3 1.0 C A:CYS260 4.8 47.6 1.0 C A:CYS241 4.9 53.5 1.0 CA A:ALA240 4.9 58.3 1.0 CG1 A:ILE259 4.9 42.0 1.0 N A:ALA240 4.9 58.2 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:68.0 occ:1.00 ND1 A:HIS257 2.2 60.9 1.0 SG A:CYS289 2.2 61.9 1.0 SG A:CYS293 2.4 73.3 1.0 SG A:CYS253 2.4 57.5 1.0 CG A:HIS257 3.0 59.1 1.0 CB A:CYS289 3.1 60.7 1.0 CE1 A:HIS257 3.2 61.6 1.0 CB A:CYS253 3.2 61.0 1.0 CB A:HIS257 3.2 55.5 1.0 CB A:CYS293 3.4 77.3 1.0 CB A:ALA291 4.1 72.5 1.0 CD2 A:HIS257 4.1 59.4 1.0 NE2 A:HIS257 4.2 61.1 1.0 N A:HIS257 4.3 56.8 1.0 CA A:HIS257 4.4 55.4 1.0 CA A:CYS289 4.6 59.8 1.0 CA A:CYS293 4.7 78.5 1.0 CB A:PHE251 4.7 53.4 1.0 CA A:CYS253 4.7 61.9 1.0 N A:CYS293 4.8 76.7 1.0 N A:ALA291 5.0 69.3 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:0.3 occ:1.00 SG A:CYS352 2.7 0.6 1.0 SG A:CYS337 3.0 0.6 1.0 SG A:CYS332 3.1 0.7 1.0 CB A:CYS332 3.2 0.6 1.0 CB A:CYS360 3.3 0.2 1.0 CB A:CYS352 3.4 0.4 1.0 CB A:ARG334 3.5 0.8 1.0 SG A:CYS360 3.8 1.0 1.0 N A:ARG334 4.5 1.0 1.0 CE2 A:PHE364 4.6 0.5 1.0 CB A:PHE362 4.6 0.8 1.0 CA A:CYS332 4.6 0.9 1.0 CA A:ARG334 4.6 0.3 1.0 CA A:CYS360 4.7 0.0 1.0 CB A:CYS337 4.7 0.0 1.0 CA A:CYS352 4.9 0.0 1.0 C A:CYS332 4.9 0.7 1.0 O A:PHE362 5.0 0.7 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:0.9 occ:1.00 SG A:CYS365 2.1 0.4 1.0 SG A:CYS368 2.4 0.3 1.0 NE2 A:HIS373 3.0 0.4 1.0 CB A:CYS365 3.0 0.1 1.0 CE1 A:HIS373 3.0 0.2 1.0 SG A:CYS377 3.3 0.9 1.0 CB A:CYS368 3.3 0.7 1.0 CB A:CYS377 3.4 0.1 1.0 N A:CYS368 3.5 0.1 1.0 CA A:CYS377 3.6 0.4 1.0 CA A:CYS368 4.0 1.0 1.0 CB A:ASP367 4.2 0.8 1.0 N A:CYS377 4.3 0.6 1.0 CD2 A:HIS373 4.3 0.2 1.0 ND1 A:HIS373 4.4 0.8 1.0 CA A:CYS365 4.5 0.1 1.0 C A:ASP367 4.5 0.3 1.0 N A:ASP367 4.6 0.0 1.0 C A:CYS368 4.7 0.4 1.0 CA A:ASP367 4.7 0.4 1.0 N A:LYS369 4.8 0.7 1.0 C A:CYS377 4.9 0.3 1.0 C A:CYS365 4.9 0.1 1.0 OD2 A:ASP367 5.0 0.4 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:61.8 occ:1.00 SG A:CYS441 2.3 70.7 1.0 SG A:CYS418 2.3 54.9 1.0 SG A:CYS436 2.3 55.8 1.0 SG A:CYS421 2.4 61.4 1.0 CB A:CYS418 3.2 54.7 1.0 CB A:CYS421 3.3 64.2 1.0 CB A:CYS436 3.3 58.7 1.0 CB A:CYS441 3.4 70.8 1.0 N A:CYS421 3.8 60.1 1.0 CA A:CYS421 4.1 64.1 1.0 CB A:GLN438 4.5 65.9 1.0 N A:LYS442 4.6 60.8 1.0 N A:LEU443 4.6 48.8 1.0 CA A:CYS418 4.6 53.5 1.0 CB A:LEU443 4.6 43.2 1.0 CB A:ARG420 4.7 48.1 1.0 C A:CYS421 4.8 66.3 1.0 CA A:CYS436 4.8 58.4 1.0 CA A:CYS441 4.8 69.4 1.0 N A:ASN422 4.9 68.8 1.0 C A:ARG420 4.9 55.5 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:37.5 occ:1.00 SG A:CYS449 2.3 38.1 1.0 SG A:CYS446 2.3 45.1 1.0 NE2 A:HIS461 2.4 40.8 1.0 SG A:CYS457 2.4 40.9 1.0 CB A:CYS449 3.2 40.3 1.0 CB A:CYS457 3.2 40.3 1.0 CD2 A:HIS461 3.2 40.5 1.0 CB A:CYS446 3.3 42.6 1.0 CE1 A:HIS461 3.4 41.6 1.0 N A:CYS449 3.7 42.2 1.0 CA A:CYS457 3.8 40.4 1.0 CA A:CYS449 4.1 41.5 1.0 CG A:HIS461 4.4 41.7 1.0 ND1 A:HIS461 4.4 41.6 1.0 CB A:ASN448 4.5 44.8 1.0 OD1 A:ASN448 4.5 46.0 1.0 C A:ASN448 4.7 43.2 1.0 CA A:CYS446 4.7 41.5 1.0 SG A:CYS451 4.8 48.0 1.0 N A:CYS457 4.8 40.8 1.0 C A:CYS457 4.9 41.1 1.0 CG A:ASN448 4.9 46.5 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:43.0 occ:1.00 NE2 B:HIS215 2.0 45.5 1.0 SG B:CYS154 2.3 39.8 1.0 SG B:CYS150 2.4 34.2 1.0 SG B:CYS212 2.4 43.6 1.0 CD2 B:HIS215 2.8 47.2 1.0 CE1 B:HIS215 3.0 47.3 1.0 CB B:CYS150 3.0 34.1 1.0 CB B:CYS154 3.3 42.0 1.0 CB B:CYS212 3.3 46.7 1.0 CG B:HIS215 3.9 47.6 1.0 ND1 B:HIS215 4.0 48.8 1.0 N B:CYS154 4.1 42.5 1.0 CD B:PRO153 4.2 45.5 1.0 CA B:CYS154 4.3 42.4 1.0 CG B:GLN158 4.3 41.9 1.0 CB B:ALA214 4.4 51.9 1.0 O B:GLY152 4.4 43.4 1.0 CA B:CYS150 4.5 33.6 1.0 NE2 B:GLN158 4.6 44.2 1.0 C B:GLY152 4.7 43.8 1.0 CA B:CYS212 4.7 47.8 1.0 N B:PRO153 4.7 45.2 1.0 CB B:GLN158 4.9 42.1 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Parkin E3 Ubiquitin Ligase (Linker Deletion; Delta 86-130) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:65.6 occ:1.00 SG B:CYS169 2.3 63.9 1.0 SG B:CYS196 2.3 76.5 1.0 SG B:CYS166 2.3 65.5 1.0 SG B:CYS201 2.4 97.8 1.0 CB B:CYS201 3.0 96.6 1.0 CB B:CYS166 3.0 64.8 1.0 CB B:CYS196 3.3 79.8 1.0 CB B:CYS169 3.5 66.9 1.0 OG B:SER198 3.8 82.0 1.0 CB B:SER198 3.8 84.9 1.0 N B:CYS169 4.3 66.3 1.0 CA B:CYS201 4.4 97.1 1.0 CA B:CYS169 4.4 68.2 1.0 CA B:CYS166 4.5 66.2 1.0 CA B:CYS196 4.7 81.0 1.0 N B:SER198 4.8 86.2 1.0 C B:CYS201 4.8 93.4 1.0 N B:GLY203 4.9 82.2 1.0 OG1 B:THR173 4.9 82.7 1.0 CA B:SER198 4.9 87.0 1.0 O B:CYS166 4.9 66.7 1.0 O B:CYS201 5.0 92.1 1.0 C B:CYS166 5.0 65.2 1.0

V.Sauve, A.Lilov, M.Seirafi, M.Vranas, S.Rasool, G.Kozlov, T.Sprules, J.Wang, J.F.Trempe, K.Gehring. A Ubl/Ubiquitin Switch in the Activation of Parkin. Embo J. V. 34 2492 2015.
ISSN: ESSN 1460-2075
PubMed: 26254305
DOI: 10.15252/EMBJ.201592237