Zinc in PDB 4k95: Crystal Structure of Parkin

The structure of Crystal Structure of Parkin, PDB code: 4k95 was solved by M.Seirafi, M.Menade, V.Sauve, G.Kozlov, J.-F.Trempe, B.Nagar, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.33 / 6.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	208.598, 277.439, 125.891, 90.00, 90.00, 90.00
R / Rfree (%)	30.7 / 32.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 96;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Parkin (pdb code 4k95). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 96 binding sites of Zinc where determined in the Crystal Structure of Parkin, PDB code: 4k95:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:40.6 occ:1.00 NE2 A:HIS215 2.0 40.6 1.0 SG A:CYS150 2.4 40.6 1.0 SG A:CYS154 2.4 40.6 1.0 SG A:CYS212 2.4 40.6 1.0 CD2 A:HIS215 2.9 40.6 1.0 CE1 A:HIS215 3.0 40.6 1.0 CB A:CYS150 3.2 40.6 1.0 CB A:CYS212 3.2 40.6 1.0 CB A:CYS154 3.3 40.6 1.0 ND1 A:HIS215 4.0 40.6 1.0 CG A:HIS215 4.0 40.6 1.0 N A:CYS154 4.1 40.6 1.0 CA A:CYS154 4.3 40.6 1.0 CG A:GLN158 4.4 40.6 1.0 CD A:PRO153 4.5 40.6 1.0 CB A:ALA214 4.6 40.6 1.0 CA A:CYS150 4.6 40.6 1.0 CA A:CYS212 4.6 40.6 1.0 N A:PRO153 4.7 40.6 1.0 CG A:PRO153 4.7 40.6 1.0 NE2 A:GLN158 4.8 40.6 1.0 C A:GLY152 4.9 40.6 1.0 O A:GLY152 4.9 40.6 1.0 N A:ALA214 5.0 40.6 1.0

Zinc binding site 2 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:40.6 occ:1.00 SG A:CYS169 2.3 40.6 1.0 SG A:CYS166 2.3 40.6 1.0 SG A:CYS196 2.4 40.6 1.0 SG A:CYS201 2.4 40.6 1.0 CB A:CYS166 2.8 40.6 1.0 CB A:CYS196 3.2 40.6 1.0 CB A:CYS169 3.2 40.6 1.0 CB A:CYS201 3.6 40.6 1.0 N A:CYS169 3.6 40.6 1.0 CA A:CYS169 4.0 40.6 1.0 CA A:CYS166 4.3 40.6 1.0 CB A:SER198 4.4 40.6 1.0 OG1 A:THR173 4.4 40.6 1.0 CA A:GLY203 4.6 40.6 1.0 CA A:CYS196 4.6 40.6 1.0 CB A:THR168 4.6 40.6 1.0 N A:GLY203 4.6 40.6 1.0 C A:CYS169 4.8 40.6 1.0 C A:THR168 4.8 40.6 1.0 CA A:CYS201 4.9 40.6 1.0 C A:CYS166 5.0 40.6 1.0 O A:GLY203 5.0 40.6 1.0 N A:ARG170 5.0 40.6 1.0

Zinc binding site 3 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:40.6 occ:1.00 SG A:CYS238 2.3 40.6 1.0 SG A:CYS260 2.4 40.6 1.0 SG A:CYS263 2.4 40.6 1.0 SG A:CYS241 2.4 40.6 1.0 CB A:CYS241 3.1 40.6 1.0 CB A:CYS238 3.2 40.6 1.0 CB A:CYS263 3.3 40.6 1.0 CB A:CYS260 3.6 40.6 1.0 N A:CYS241 3.7 40.6 1.0 CA A:CYS241 4.0 40.6 1.0 N A:CYS260 4.2 40.6 1.0 N A:CYS263 4.3 40.6 1.0 CA A:CYS263 4.4 40.6 1.0 CA A:CYS260 4.4 40.6 1.0 C A:ALA240 4.6 40.6 1.0 CA A:CYS238 4.6 40.6 1.0 CB A:ALA240 4.7 40.6 1.0 O A:CYS260 4.8 40.6 1.0 C A:CYS241 4.8 40.6 1.0 N A:ALA240 4.8 40.6 1.0 C A:CYS260 4.9 40.6 1.0 CA A:ALA240 4.9 40.6 1.0 N A:THR242 5.0 40.6 1.0

Zinc binding site 4 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:40.6 occ:1.00 ND1 A:HIS257 2.0 40.6 1.0 SG A:CYS253 2.2 40.6 1.0 SG A:CYS289 2.4 40.6 1.0 SG A:CYS293 2.4 40.6 1.0 CE1 A:HIS257 2.9 40.6 1.0 CG A:HIS257 3.1 40.6 1.0 CB A:CYS253 3.2 40.6 1.0 CB A:CYS289 3.4 40.6 1.0 CB A:HIS257 3.5 40.6 1.0 CB A:CYS293 3.6 40.6 1.0 NE2 A:HIS257 4.1 40.6 1.0 N A:HIS257 4.1 40.6 1.0 CD2 A:HIS257 4.2 40.6 1.0 CB A:ALA291 4.3 40.6 1.0 CA A:HIS257 4.4 40.6 1.0 CA A:CYS253 4.7 40.6 1.0 CA A:CYS289 4.8 40.6 1.0 CA A:CYS293 4.8 40.6 1.0 N A:CYS293 4.8 40.6 1.0 N A:ARG256 5.0 40.6 1.0

Zinc binding site 5 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:0.4 occ:1.00 SG A:CYS332 2.3 0.4 1.0 SG A:CYS360 2.3 0.4 1.0 SG A:CYS352 2.4 0.4 1.0 SG A:CYS337 2.4 0.4 1.0 CB A:CYS337 3.1 0.4 1.0 CB A:CYS332 3.2 0.4 1.0 CB A:CYS352 3.3 0.4 1.0 CB A:CYS360 3.4 0.4 1.0 N A:CYS360 3.6 0.4 1.0 CA A:CYS360 4.1 0.4 1.0 CA A:CYS337 4.5 0.4 1.0 CA A:CYS332 4.6 0.4 1.0 CA A:CYS352 4.7 0.4 1.0 C A:GLY359 4.7 0.4 1.0 CB A:ALA339 4.8 0.4 1.0 N A:GLY338 4.8 0.4 1.0 C A:CYS360 4.8 0.4 1.0 CB A:ARG334 4.9 0.4 1.0 N A:ALA339 4.9 0.4 1.0 CB A:PHE362 4.9 0.4 1.0 CA A:GLY359 4.9 0.4 1.0 C A:CYS337 4.9 0.4 1.0 N A:GLY361 5.0 0.4 1.0

Zinc binding site 6 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:0.4 occ:1.00 NE2 A:HIS373 2.1 0.4 1.0 SG A:CYS368 2.3 0.4 1.0 SG A:CYS365 2.3 0.4 1.0 SG A:CYS377 2.4 0.4 1.0 CE1 A:HIS373 2.8 0.4 1.0 CB A:CYS365 2.9 0.4 1.0 CD2 A:HIS373 3.2 0.4 1.0 CB A:CYS368 3.4 0.4 1.0 CB A:CYS377 3.5 0.4 1.0 N A:CYS368 3.8 0.4 1.0 ND1 A:HIS373 3.9 0.4 1.0 CG A:HIS373 4.1 0.4 1.0 CA A:CYS377 4.1 0.4 1.0 CA A:CYS368 4.2 0.4 1.0 CA A:CYS365 4.4 0.4 1.0 N A:CYS377 4.5 0.4 1.0 NE A:ARG348 4.5 0.4 1.0 CB A:ASP367 4.8 0.4 1.0 C A:CYS365 4.8 0.4 1.0 O A:CYS365 4.9 0.4 1.0 C A:ASP367 4.9 0.4 1.0

Zinc binding site 7 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:40.6 occ:1.00 SG A:CYS436 2.3 40.6 1.0 SG A:CYS421 2.3 40.6 1.0 SG A:CYS441 2.4 40.6 1.0 SG A:CYS418 2.4 40.6 1.0 CB A:CYS436 2.9 40.6 1.0 CB A:CYS441 3.1 40.6 1.0 CB A:CYS418 3.2 40.6 1.0 CB A:CYS421 3.5 40.6 1.0 N A:CYS421 4.3 40.6 1.0 CA A:CYS436 4.3 40.6 1.0 CB A:GLN438 4.3 40.6 1.0 N A:LEU443 4.4 40.6 1.0 N A:LYS442 4.4 40.6 1.0 CA A:CYS421 4.4 40.6 1.0 CB A:LEU443 4.5 40.6 1.0 CA A:CYS441 4.5 40.6 1.0 C A:CYS441 4.7 40.6 1.0 CG A:GLN438 4.7 40.6 1.0 CA A:CYS418 4.7 40.6 1.0 C A:CYS436 4.9 40.6 1.0 C A:CYS421 5.0 40.6 1.0

Zinc binding site 8 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:40.6 occ:1.00 NE2 A:HIS461 2.1 40.6 1.0 SG A:CYS457 2.3 40.6 1.0 SG A:CYS446 2.3 40.6 1.0 SG A:CYS449 2.4 40.6 1.0 CE1 A:HIS461 3.0 40.6 1.0 CD2 A:HIS461 3.2 40.6 1.0 CB A:CYS449 3.2 40.6 1.0 CB A:CYS457 3.2 40.6 1.0 CB A:CYS446 3.3 40.6 1.0 N A:CYS449 3.9 40.6 1.0 CA A:CYS457 4.1 40.6 1.0 ND1 A:HIS461 4.1 40.6 1.0 CA A:CYS449 4.2 40.6 1.0 CG A:HIS461 4.3 40.6 1.0 SG A:CYS451 4.6 40.6 1.0 CA A:CYS446 4.7 40.6 1.0 CB A:ASN448 4.8 40.6 1.0 OD1 A:ASN448 5.0 40.6 1.0 O A:CYS457 5.0 40.6 1.0 C A:ASN448 5.0 40.6 1.0

Zinc binding site 9 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:70.6 occ:1.00 NE2 B:HIS215 2.0 70.6 1.0 SG B:CYS150 2.4 70.6 1.0 SG B:CYS154 2.4 70.6 1.0 SG B:CYS212 2.4 70.6 1.0 CD2 B:HIS215 2.9 70.6 1.0 CE1 B:HIS215 3.0 70.6 1.0 CB B:CYS150 3.2 70.6 1.0 CB B:CYS212 3.2 70.6 1.0 CB B:CYS154 3.3 70.6 1.0 ND1 B:HIS215 4.0 70.6 1.0 CG B:HIS215 4.0 70.6 1.0 N B:CYS154 4.1 70.6 1.0 CA B:CYS154 4.3 70.6 1.0 CG B:GLN158 4.4 70.6 1.0 CD B:PRO153 4.5 70.6 1.0 CB B:ALA214 4.6 70.6 1.0 CA B:CYS150 4.6 70.6 1.0 CA B:CYS212 4.6 70.6 1.0 N B:PRO153 4.7 70.6 1.0 CG B:PRO153 4.7 70.6 1.0 NE2 B:GLN158 4.9 70.6 1.0 C B:GLY152 4.9 70.6 1.0 O B:GLY152 4.9 70.6 1.0 N B:ALA214 5.0 70.6 1.0

Zinc binding site 10 out of 96 in the Crystal Structure of Parkin


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:70.6 occ:1.00 SG B:CYS169 2.3 70.6 1.0 SG B:CYS166 2.3 70.6 1.0 SG B:CYS196 2.4 70.6 1.0 SG B:CYS201 2.4 70.6 1.0 CB B:CYS166 2.8 70.6 1.0 CB B:CYS196 3.2 70.6 1.0 CB B:CYS169 3.2 70.6 1.0 CB B:CYS201 3.6 70.6 1.0 N B:CYS169 3.6 70.6 1.0 CA B:CYS169 4.0 70.6 1.0 CA B:CYS166 4.3 70.6 1.0 CB B:SER198 4.4 70.6 1.0 OG1 B:THR173 4.4 70.6 1.0 CA B:GLY203 4.6 70.6 1.0 CA B:CYS196 4.6 70.6 1.0 CB B:THR168 4.6 70.6 1.0 N B:GLY203 4.6 70.6 1.0 C B:CYS169 4.8 70.6 1.0 C B:THR168 4.8 70.6 1.0 CA B:CYS201 4.9 70.6 1.0 C B:CYS166 5.0 70.6 1.0 O B:GLY203 5.0 70.6 1.0 N B:ARG170 5.0 70.6 1.0

J.F.Trempe, V.Sauve, K.Grenier, M.Seirafi, M.Y.Tang, M.Menade, S.Al-Abdul-Wahid, J.Krett, K.Wong, G.Kozlov, B.Nagar, E.A.Fon, K.Gehring. Structure of Parkin Reveals Mechanisms For Ubiquitin Ligase Activation. Science V. 340 1451 2013.
ISSN: ISSN 0036-8075
PubMed: 23661642
DOI: 10.1126/SCIENCE.1237908