Zinc in PDB 4k7d: Crystal Structure of Parkin C-Terminal Ring Domains

The structure of Crystal Structure of Parkin C-Terminal Ring Domains, PDB code: 4k7d was solved by V.Sauve, J.-F.Trempe, M.Menade, K.Gehring, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.31 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.700, 106.625, 154.216, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.3

The structure of Crystal Structure of Parkin C-Terminal Ring Domains also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Parkin C-Terminal Ring Domains (pdb code 4k7d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Crystal Structure of Parkin C-Terminal Ring Domains, PDB code: 4k7d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:58.7 occ:1.00 NE2 A:HIS215 2.1 44.9 1.0 SG A:CYS154 2.3 45.1 1.0 SG A:CYS212 2.3 35.4 1.0 SG A:CYS150 2.4 41.5 1.0 CD2 A:HIS215 2.9 41.1 1.0 CB A:CYS154 3.1 43.5 1.0 CE1 A:HIS215 3.1 43.2 1.0 CB A:CYS212 3.2 33.2 1.0 CB A:CYS150 3.2 36.2 1.0 N A:CYS154 4.0 35.1 1.0 CG A:HIS215 4.1 37.6 1.0 CA A:CYS154 4.1 43.3 1.0 CB A:ALA214 4.2 43.4 1.0 CD A:PRO153 4.2 34.2 1.0 ND1 A:HIS215 4.2 36.8 1.0 CG A:GLN158 4.5 39.6 1.0 N A:PRO153 4.6 43.6 1.0 CA A:CYS212 4.6 35.8 1.0 CA A:CYS150 4.7 40.6 1.0 O A:GLY152 4.7 43.6 1.0 C A:GLY152 4.7 43.7 1.0 CG A:PRO153 5.0 29.3 1.0

Zinc binding site 2 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:83.4 occ:1.00 SG A:CYS169 2.3 68.5 1.0 SG A:CYS166 2.3 63.2 1.0 SG A:CYS196 2.4 69.9 1.0 SG A:CYS201 2.4 77.5 1.0 CB A:CYS166 2.9 59.5 1.0 CB A:CYS169 3.3 66.8 1.0 CB A:CYS196 3.3 70.7 1.0 CB A:CYS201 3.5 77.2 1.0 N A:CYS169 3.7 68.5 1.0 CA A:CYS169 4.1 67.8 1.0 OG A:SER198 4.4 72.4 1.0 CA A:CYS166 4.4 54.2 1.0 CB A:SER198 4.4 72.3 1.0 CB A:THR168 4.5 72.8 1.0 OG1 A:THR173 4.5 69.7 1.0 CA A:GLY203 4.7 69.3 1.0 CA A:CYS196 4.7 71.0 1.0 N A:GLY203 4.7 73.6 1.0 C A:THR168 4.8 70.6 1.0 CA A:CYS201 4.8 79.6 1.0 C A:CYS166 4.9 63.1 1.0 C A:CYS169 4.9 63.5 1.0 O A:CYS166 4.9 67.0 1.0 CG2 A:THR168 4.9 73.2 1.0 N A:ARG170 5.0 62.8 1.0

Zinc binding site 3 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:84.9 occ:1.00 SG A:CYS263 2.4 65.5 1.0 SG A:CYS238 2.4 69.2 1.0 SG A:CYS260 2.5 63.4 1.0 SG A:CYS241 2.5 83.3 1.0 CB A:CYS263 3.1 59.2 1.0 CB A:CYS238 3.2 67.3 1.0 CB A:CYS260 3.4 60.7 1.0 CB A:CYS241 3.7 73.8 1.0 N A:CYS241 3.8 71.1 1.0 N A:CYS260 4.0 57.7 1.0 CA A:CYS260 4.2 60.3 1.0 CA A:CYS263 4.3 61.9 1.0 N A:CYS263 4.3 60.9 1.0 CA A:CYS241 4.3 74.2 1.0 CB A:ALA240 4.4 65.8 1.0 CA A:CYS238 4.6 63.5 1.0 N A:ALA240 4.8 56.1 1.0 C A:ALA240 4.8 70.1 1.0 O A:CYS260 4.8 59.1 1.0 C A:CYS260 4.8 58.8 1.0 CA A:ALA240 4.9 61.8 1.0

Zinc binding site 4 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:82.2 occ:1.00 ND1 A:HIS257 2.1 76.6 1.0 SG A:CYS293 2.4 65.4 1.0 SG A:CYS289 2.4 63.3 1.0 SG A:CYS253 2.4 58.6 1.0 CE1 A:HIS257 3.0 76.3 1.0 CB A:CYS289 3.0 53.1 1.0 CG A:HIS257 3.1 71.4 1.0 CB A:CYS293 3.5 67.3 1.0 CB A:HIS257 3.5 65.7 1.0 CB A:CYS253 3.6 56.7 1.0 CB A:ALA291 3.9 63.4 1.0 NE2 A:HIS257 4.1 74.2 1.0 N A:HIS257 4.1 59.3 1.0 CD2 A:HIS257 4.2 72.8 1.0 CA A:HIS257 4.4 61.0 1.0 CA A:CYS289 4.5 54.9 1.0 CA A:CYS293 4.7 63.5 1.0 CB A:PHE251 4.8 47.3 1.0 N A:CYS293 4.8 58.5 1.0 CB A:HIS255 4.9 74.5 1.0 N A:ALA291 4.9 65.2 1.0 CA A:ALA291 5.0 67.0 1.0

Zinc binding site 5 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:54.9 occ:1.00 SG A:CYS332 2.2 38.8 1.0 SG A:CYS352 2.2 46.5 1.0 SG A:CYS337 2.3 39.5 1.0 SG A:CYS360 2.4 41.0 1.0 CB A:CYS332 3.0 38.1 1.0 CB A:CYS352 3.1 34.8 1.0 CB A:CYS337 3.2 38.2 1.0 CB A:CYS360 3.2 42.7 1.0 N A:CYS360 3.9 44.8 1.0 CA A:CYS360 4.1 44.6 1.0 CA A:CYS332 4.5 34.9 1.0 CA A:CYS352 4.6 37.0 1.0 CB A:PHE362 4.6 39.8 1.0 CA A:CYS337 4.6 44.9 1.0 N A:GLY338 4.7 35.9 1.0 CB A:ALA339 4.7 28.2 1.0 CD A:ARG334 4.7 41.5 1.0 N A:ALA339 4.8 36.3 1.0 C A:CYS360 4.8 43.5 1.0 CB A:ARG334 4.9 39.8 1.0 C A:GLY359 4.9 41.7 1.0 N A:GLY361 4.9 38.0 1.0 C A:CYS337 4.9 41.1 1.0

Zinc binding site 6 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:85.5 occ:1.00 NE2 A:HIS373 2.0 79.5 1.0 SG A:CYS365 2.4 64.0 1.0 SG A:CYS368 2.4 61.2 1.0 SG A:CYS377 2.4 85.0 1.0 CD2 A:HIS373 2.8 72.5 1.0 CE1 A:HIS373 3.1 81.9 1.0 CB A:CYS365 3.1 54.9 1.0 CB A:CYS368 3.4 44.2 1.0 CB A:CYS377 3.6 87.2 1.0 N A:CYS368 3.8 59.7 1.0 NH1 A:ARG348 3.8 74.0 1.0 CA A:CYS377 3.9 91.0 1.0 CG A:HIS373 4.0 69.5 1.0 ND1 A:HIS373 4.1 76.9 1.0 N A:CYS377 4.2 91.7 1.0 CA A:CYS368 4.2 55.1 1.0 CA A:CYS365 4.6 48.0 1.0 CB A:ASP367 4.6 70.8 1.0 C A:ASP367 4.8 57.5 1.0 N A:ASP367 4.9 61.4 1.0 C A:GLU376 4.9 89.5 1.0 C A:CYS365 4.9 50.2 1.0 CA A:ASP367 5.0 61.3 1.0

Zinc binding site 7 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:62.7 occ:1.00 SG A:CYS441 2.3 45.5 1.0 SG A:CYS418 2.3 43.5 1.0 SG A:CYS436 2.3 50.0 1.0 SG A:CYS421 2.5 51.7 1.0 CB A:CYS441 3.2 42.1 1.0 CB A:CYS418 3.2 47.1 1.0 CB A:CYS421 3.2 33.2 1.0 CB A:CYS436 3.2 57.0 1.0 N A:CYS421 3.6 45.3 1.0 CA A:CYS421 4.0 39.8 1.0 CB A:LEU443 4.4 43.9 1.0 CB A:ARG420 4.6 39.5 1.0 CA A:CYS441 4.6 49.4 1.0 N A:LEU443 4.6 46.7 1.0 CA A:CYS418 4.6 44.7 1.0 N A:LYS442 4.7 56.8 1.0 CA A:CYS436 4.7 54.3 1.0 N A:ASN422 4.7 47.5 1.0 C A:CYS421 4.7 49.0 1.0 C A:ARG420 4.7 44.7 1.0 CB A:GLN438 4.9 52.8 1.0 C A:CYS441 4.9 57.8 1.0 CA A:ARG420 5.0 41.5 1.0 N A:ARG420 5.0 43.5 1.0

Zinc binding site 8 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:57.6 occ:1.00 NE2 A:HIS461 2.1 40.6 1.0 SG A:CYS446 2.3 40.1 1.0 SG A:CYS449 2.3 50.6 1.0 SG A:CYS457 2.4 38.5 1.0 CE1 A:HIS461 3.0 39.5 1.0 CD2 A:HIS461 3.1 39.0 1.0 CB A:CYS449 3.3 53.6 1.0 CB A:CYS446 3.4 40.1 1.0 CB A:CYS457 3.6 43.3 1.0 N A:CYS449 4.0 46.2 1.0 ND1 A:HIS461 4.2 42.7 1.0 CG A:HIS461 4.3 40.5 1.0 CA A:CYS449 4.3 50.8 1.0 CA A:CYS457 4.3 37.5 1.0 CB A:ASN448 4.5 40.3 1.0 SG A:CYS451 4.6 43.3 1.0 CA A:CYS446 4.8 36.3 1.0 OD1 A:ASN448 4.8 49.4 1.0 C A:ASN448 4.9 46.8 1.0

Zinc binding site 9 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:53.0 occ:1.00 NE2 B:HIS215 2.1 40.2 1.0 SG B:CYS212 2.3 34.1 1.0 SG B:CYS154 2.4 37.5 1.0 SG B:CYS150 2.5 35.8 1.0 CD2 B:HIS215 2.8 33.6 1.0 CE1 B:HIS215 3.1 34.0 1.0 CB B:CYS150 3.2 37.0 1.0 CB B:CYS212 3.2 29.2 1.0 CB B:CYS154 3.3 40.3 1.0 O B:HOH609 3.8 33.6 1.0 CG B:HIS215 4.0 32.5 1.0 N B:CYS154 4.1 36.3 1.0 ND1 B:HIS215 4.1 31.6 1.0 CA B:CYS154 4.3 37.9 1.0 CG B:GLN158 4.4 29.9 1.0 CB B:ALA214 4.4 39.2 1.0 CD B:PRO153 4.4 26.8 1.0 CA B:CYS150 4.6 35.5 1.0 CA B:CYS212 4.7 39.7 1.0 CG B:PRO153 4.7 24.4 1.0 N B:PRO153 4.8 33.9 1.0 N B:ALA214 5.0 46.0 1.0 CB B:GLN158 5.0 33.1 1.0

Zinc binding site 10 out of 24 in the Crystal Structure of Parkin C-Terminal Ring Domains


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 C-Terminal Ring Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:0.9 occ:1.00 SG B:CYS166 2.3 87.9 1.0 SG B:CYS196 2.3 98.5 1.0 SG B:CYS201 2.3 0.9 1.0 SG B:CYS169 2.4 93.4 1.0 CB B:CYS196 2.8 85.3 1.0 CB B:CYS166 3.0 79.7 1.0 CB B:CYS201 3.2 0.1 1.0 CB B:CYS169 3.2 82.3 1.0 OG1 B:THR168 3.5 94.2 1.0 N B:CYS169 3.8 83.0 1.0 CA B:CYS169 4.1 80.7 1.0 OG1 B:THR173 4.3 80.8 1.0 CA B:CYS196 4.3 85.8 1.0 CA B:CYS166 4.5 71.6 1.0 CA B:CYS201 4.6 99.3 1.0 O B:CYS201 4.8 94.0 1.0 C B:THR168 4.8 87.7 1.0 CB B:THR168 4.8 90.2 1.0 C B:CYS201 4.9 97.3 1.0 CA B:GLY203 4.9 0.9 1.0 N B:GLY203 4.9 0.5 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