Zinc in PDB 5c9v: Structure of Human Parkin G319A

The structure of Structure of Human Parkin G319A, PDB code: 5c9v was solved by T.Wauer, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.68 / 2.35
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	169.360, 169.360, 96.990, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 22.9

The binding sites of Zinc atom in the Structure of Human Parkin G319A (pdb code 5c9v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Human Parkin G319A, PDB code: 5c9v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:38.7 occ:1.00 NE2 A:HIS215 2.0 34.7 1.0 SG A:CYS150 2.3 37.6 1.0 SG A:CYS212 2.3 39.6 1.0 SG A:CYS154 2.4 43.5 1.0 CD2 A:HIS215 2.8 35.2 1.0 CB A:CYS150 3.0 27.9 1.0 CE1 A:HIS215 3.0 35.1 1.0 CB A:CYS212 3.2 39.6 1.0 CB A:CYS154 3.2 33.7 1.0 CG A:HIS215 4.0 35.8 1.0 O A:HOH653 4.0 36.4 1.0 ND1 A:HIS215 4.0 34.7 1.0 N A:CYS154 4.1 42.2 1.0 CA A:CYS154 4.2 40.6 1.0 CD A:PRO153 4.4 48.1 1.0 CG A:GLN158 4.4 36.4 1.0 CA A:CYS150 4.5 34.9 1.0 CB A:ALA214 4.5 36.3 1.0 CA A:CYS212 4.6 39.2 1.0 N A:PRO153 4.6 49.0 1.0 O A:GLY152 4.7 51.5 1.0 NE2 A:GLN158 4.7 38.3 1.0 C A:GLY152 4.8 49.7 1.0 CB A:GLN158 5.0 36.4 1.0

Zinc binding site 2 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:56.8 occ:1.00 ND1 A:HIS257 2.1 57.0 1.0 SG A:CYS293 2.3 53.0 1.0 SG A:CYS253 2.3 54.4 1.0 SG A:CYS289 2.4 55.9 1.0 CE1 A:HIS257 2.8 57.7 1.0 CB A:CYS289 3.2 46.3 1.0 CB A:CYS253 3.2 54.4 1.0 CG A:HIS257 3.2 55.8 1.0 CB A:CYS293 3.3 59.8 1.0 CB A:HIS257 3.7 52.8 1.0 NE2 A:HIS257 4.0 58.1 1.0 CB A:ALA291 4.1 52.6 1.0 CD2 A:HIS257 4.2 56.9 1.0 N A:HIS257 4.5 57.4 1.0 CA A:CYS293 4.6 63.2 1.0 N A:CYS293 4.6 59.5 1.0 CA A:CYS289 4.6 48.4 1.0 CA A:CYS253 4.6 56.6 1.0 CB A:SER255 4.7 61.5 1.0 CA A:HIS257 4.8 53.5 1.0 CB A:PHE251 4.9 48.9 1.0 N A:ALA291 4.9 49.8 1.0 OG A:SER255 5.0 64.1 1.0

Zinc binding site 3 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:40.0 occ:1.00 SG A:CYS446 2.3 33.4 1.0 SG A:CYS457 2.3 39.7 1.0 NE2 A:HIS461 2.3 37.9 1.0 SG A:CYS449 2.4 41.9 1.0 CB A:CYS457 3.1 38.4 1.0 CB A:CYS446 3.2 37.2 1.0 CB A:CYS449 3.2 31.7 1.0 CD2 A:HIS461 3.2 37.0 1.0 CE1 A:HIS461 3.3 35.5 1.0 N A:CYS449 3.9 42.8 1.0 CA A:CYS457 3.9 35.0 1.0 CA A:CYS449 4.2 41.3 1.0 CG A:HIS461 4.4 35.0 1.0 ND1 A:HIS461 4.4 35.1 1.0 CB A:ASN448 4.6 45.7 1.0 CA A:CYS446 4.6 38.9 1.0 OD1 A:ASN448 4.8 51.3 1.0 SG A:CYS451 4.8 46.2 1.0 N A:CYS457 4.9 36.3 1.0 C A:ASN448 4.9 42.6 1.0

Zinc binding site 4 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:55.5 occ:1.00 SG A:CYS169 2.3 54.9 1.0 SG A:CYS196 2.3 55.5 1.0 SG A:CYS201 2.3 61.4 1.0 SG A:CYS166 2.4 51.0 1.0 CB A:CYS166 3.0 46.9 1.0 CB A:CYS201 3.2 68.1 1.0 CB A:CYS169 3.3 57.5 1.0 CB A:CYS196 3.4 63.1 1.0 N A:CYS169 3.8 55.7 1.0 OG A:SER198 3.8 83.1 1.0 CA A:CYS169 4.1 58.3 1.0 CB A:SER198 4.2 84.5 1.0 OG1 A:THR173 4.3 59.7 1.0 CA A:GLY203 4.4 57.6 1.0 CA A:CYS166 4.5 45.6 1.0 N A:GLY203 4.5 61.5 1.0 CA A:CYS201 4.6 69.3 1.0 CB A:THR168 4.7 59.1 1.0 CA A:CYS196 4.7 62.0 1.0 C A:THR168 4.8 52.2 1.0 C A:CYS169 4.9 62.3 1.0 C A:CYS201 4.9 63.7 1.0 C A:CYS166 5.0 45.3 1.0 O A:CYS201 5.0 58.5 1.0

Zinc binding site 5 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:44.9 occ:1.00 SG A:CYS260 2.3 46.1 1.0 SG A:CYS241 2.4 49.0 1.0 SG A:CYS263 2.4 45.3 1.0 SG A:CYS238 2.4 48.4 1.0 CB A:CYS238 3.1 42.9 1.0 CB A:CYS263 3.2 43.5 1.0 CB A:CYS241 3.4 47.9 1.0 CB A:CYS260 3.4 38.3 1.0 N A:CYS241 3.8 48.1 1.0 N A:CYS260 3.9 38.7 1.0 CA A:CYS241 4.1 50.7 1.0 CA A:CYS260 4.2 38.0 1.0 N A:CYS263 4.3 43.9 1.0 CA A:CYS263 4.4 43.8 1.0 CA A:CYS238 4.6 46.8 1.0 CB A:THR240 4.7 45.7 1.0 O A:CYS260 4.7 40.5 1.0 C A:CYS260 4.8 38.0 1.0 C A:THR240 4.8 48.6 1.0 C A:CYS241 4.9 54.6 1.0 CG1 A:ILE259 4.9 38.2 1.0 N A:THR240 5.0 50.8 1.0

Zinc binding site 6 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:69.2 occ:1.00 SG A:CYS352 2.3 77.0 1.0 SG A:CYS337 2.3 63.9 1.0 SG A:CYS332 2.3 62.0 1.0 SG A:CYS360 2.4 90.5 1.0 CB A:CYS337 2.9 60.9 1.0 CB A:CYS332 3.3 57.7 1.0 CB A:CYS352 3.4 66.4 1.0 CB A:CYS360 3.5 70.9 1.0 N A:CYS360 3.8 74.4 1.0 CA A:CYS360 4.2 77.3 1.0 CA A:CYS337 4.4 66.3 1.0 CB A:ALA339 4.5 54.8 1.0 N A:GLY338 4.5 65.2 1.0 N A:ALA339 4.5 55.7 1.0 C A:GLY359 4.7 75.6 1.0 CA A:CYS352 4.8 68.6 1.0 CA A:CYS332 4.8 56.4 1.0 C A:CYS337 4.8 63.8 1.0 C A:CYS360 4.8 84.1 1.0 O A:CYS360 4.9 80.3 1.0

Zinc binding site 7 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:54.4 occ:1.00 NE2 A:HIS373 2.1 48.6 1.0 SG A:CYS368 2.3 51.4 1.0 SG A:CYS365 2.3 50.8 1.0 SG A:CYS377 2.4 56.2 1.0 CE1 A:HIS373 2.9 53.0 1.0 CB A:CYS365 3.1 55.3 1.0 CD2 A:HIS373 3.2 48.7 1.0 CB A:CYS377 3.2 47.9 1.0 CB A:CYS368 3.3 51.8 1.0 N A:CYS368 3.7 50.5 1.0 CA A:CYS377 3.9 48.0 1.0 O1 A:GOL515 3.9 82.5 1.0 ND1 A:HIS373 4.1 54.4 1.0 CA A:CYS368 4.1 49.2 1.0 CG A:HIS373 4.2 54.0 1.0 NH1 A:ARG348 4.4 58.0 1.0 CA A:CYS365 4.5 54.9 1.0 N A:CYS377 4.5 52.4 1.0 CB A:GLU367 4.5 59.3 1.0 C A:GLU367 4.6 52.9 1.0 N A:GLU367 4.8 55.6 1.0 CA A:GLU367 4.9 54.8 1.0 C A:CYS365 4.9 53.9 1.0 C A:CYS368 4.9 48.6 1.0

Zinc binding site 8 out of 8 in the Structure of Human Parkin G319A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human Parkin G319A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:42.8 occ:1.00 SG A:CYS421 2.3 43.5 1.0 SG A:CYS418 2.3 45.3 1.0 SG A:CYS436 2.3 46.1 1.0 SG A:CYS441 2.3 45.6 1.0 CB A:CYS441 3.0 41.7 1.0 CB A:CYS418 3.1 43.0 1.0 CB A:CYS421 3.3 44.6 1.0 CB A:CYS436 3.3 41.5 1.0 N A:CYS421 3.7 41.4 1.0 CA A:CYS421 4.0 43.9 1.0 N A:ARG442 4.4 49.4 1.0 CA A:CYS441 4.4 47.3 1.0 N A:LEU443 4.5 46.2 1.0 CB A:GLN438 4.5 59.0 1.0 CB A:LEU443 4.5 42.7 1.0 CA A:CYS418 4.6 40.5 1.0 C A:CYS421 4.7 45.4 1.0 CA A:CYS436 4.7 44.3 1.0 CB A:ARG420 4.7 39.9 1.0 N A:HIS422 4.7 46.0 1.0 C A:CYS441 4.8 46.3 1.0 C A:ARG420 4.8 43.6 1.0 CG A:GLN438 5.0 66.0 1.0

T.Wauer, M.Simicek, A.Schubert, D.Komander. Mechanism of Phospho-Ubiquitin-Induced Parkin Activation. Nature V. 524 370 2015.
ISSN: ESSN 1476-4687
PubMed: 26161729
DOI: 10.1038/NATURE14879