Zinc in PDB 4bm9: Structure of the Autoinhibited Parkin Catalytic Domain

The structure of Structure of the Autoinhibited Parkin Catalytic Domain, PDB code: 4bm9 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)	48.619 / 2.25
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	168.420, 168.420, 97.181, 90.00, 90.00, 120.00
R / Rfree (%)	19.03 / 21.78

The binding sites of Zinc atom in the Structure of the Autoinhibited Parkin Catalytic Domain (pdb code 4bm9). 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 the Autoinhibited Parkin Catalytic Domain, PDB code: 4bm9:
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 the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1466 b:28.3 occ:1.00 NE2 A:HIS215 2.0 26.9 1.0 SG A:CYS150 2.3 30.2 1.0 SG A:CYS212 2.3 25.9 1.0 SG A:CYS154 2.4 27.8 1.0 CD2 A:HIS215 2.9 25.4 1.0 CB A:CYS150 3.0 19.8 1.0 CE1 A:HIS215 3.1 23.9 1.0 CB A:CYS154 3.1 21.3 1.0 CB A:CYS212 3.2 28.5 1.0 N A:CYS154 3.9 39.9 1.0 CG A:HIS215 4.0 25.8 1.0 O A:HOH2009 4.1 24.5 1.0 ND1 A:HIS215 4.1 21.3 1.0 CA A:CYS154 4.2 35.8 1.0 CD A:PRO153 4.3 29.3 1.0 CG A:GLN158 4.4 26.2 1.0 CA A:CYS150 4.5 28.7 1.0 NE2 A:GLN158 4.6 37.3 1.0 CA A:CYS212 4.6 30.6 1.0 N A:PRO153 4.7 35.6 1.0 CB A:ALA214 4.7 28.8 1.0 O A:GLY152 4.7 39.7 1.0 CG A:PRO153 4.8 38.0 1.0 C A:GLY152 4.8 39.9 1.0 CB A:GLN158 5.0 22.2 1.0

Zinc binding site 2 out of 8 in the Structure of the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1467 b:48.6 occ:1.00 ND1 A:HIS257 1.8 53.1 1.0 SG A:CYS253 2.4 58.7 1.0 SG A:CYS289 2.4 52.1 1.0 CE1 A:HIS257 2.4 57.5 1.0 SG A:CYS293 2.5 52.6 1.0 CG A:HIS257 3.1 52.9 1.0 CB A:CYS289 3.2 34.3 1.0 CB A:CYS253 3.2 45.2 1.0 CB A:CYS293 3.4 48.1 1.0 NE2 A:HIS257 3.7 56.3 1.0 CB A:HIS257 3.8 44.5 1.0 CB A:ALA291 4.0 49.4 1.0 CD2 A:HIS257 4.0 55.4 1.0 N A:HIS257 4.6 45.1 1.0 N A:CYS293 4.6 53.2 1.0 CA A:CYS293 4.6 55.6 1.0 CA A:CYS289 4.7 38.1 1.0 CA A:CYS253 4.7 46.3 1.0 CB A:SER255 4.8 61.6 1.0 CA A:HIS257 4.8 43.3 1.0 OG A:SER255 4.8 65.7 1.0 N A:ALA291 4.9 42.5 1.0 CA A:ALA291 4.9 47.6 1.0 CB A:PHE251 5.0 37.5 1.0

Zinc binding site 3 out of 8 in the Structure of the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1468 b:27.0 occ:1.00 NE2 A:HIS461 2.1 32.5 1.0 SG A:CYS457 2.2 26.1 1.0 SG A:CYS446 2.3 22.9 1.0 SG A:CYS449 2.4 29.6 1.0 CE1 A:HIS461 3.0 26.2 1.0 CB A:CYS449 3.1 22.1 1.0 CB A:CYS457 3.2 17.6 1.0 CD2 A:HIS461 3.2 25.0 1.0 CB A:CYS446 3.2 27.4 1.0 N A:CYS449 3.9 34.9 1.0 CA A:CYS457 4.0 21.2 1.0 CA A:CYS449 4.1 29.8 1.0 ND1 A:HIS461 4.1 27.4 1.0 CG A:HIS461 4.3 21.9 1.0 CB A:ASN448 4.6 39.6 1.0 OD1 A:ASN448 4.6 41.0 1.0 CA A:CYS446 4.7 27.8 1.0 C A:ASN448 4.9 35.2 1.0 N A:CYS457 4.9 23.4 1.0 SG A:CYS451 4.9 38.8 1.0

Zinc binding site 4 out of 8 in the Structure of the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1469 b:38.4 occ:1.00 SG A:CYS169 2.2 39.1 1.0 SG A:CYS196 2.3 43.9 1.0 SG A:CYS201 2.3 41.1 1.0 SG A:CYS166 2.4 37.1 1.0 CB A:CYS166 3.1 30.5 1.0 CB A:CYS201 3.1 43.6 1.0 CB A:CYS169 3.3 50.0 1.0 CB A:CYS196 3.3 44.0 1.0 N A:CYS169 3.8 47.0 1.0 OG1 A:THR168 3.8 73.8 1.0 CA A:CYS169 4.1 49.2 1.0 OG1 A:THR173 4.3 44.2 1.0 CB A:SER198 4.3 62.6 1.0 CA A:GLY203 4.4 37.9 1.0 OG A:SER198 4.4 57.4 1.0 N A:GLY203 4.5 40.7 1.0 CA A:CYS201 4.5 48.1 1.0 CA A:CYS166 4.6 29.4 1.0 CA A:CYS196 4.6 47.3 1.0 C A:CYS201 4.8 45.9 1.0 C A:THR168 4.9 42.7 1.0 C A:CYS169 5.0 52.6 1.0 O A:GLY203 5.0 44.9 1.0

Zinc binding site 5 out of 8 in the Structure of the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1470 b:36.0 occ:1.00 SG A:CYS260 2.3 34.3 1.0 SG A:CYS263 2.3 36.0 1.0 SG A:CYS238 2.3 28.4 1.0 SG A:CYS241 2.4 40.8 1.0 CB A:CYS238 3.1 32.7 1.0 CB A:CYS263 3.2 27.2 1.0 CB A:CYS241 3.2 39.6 1.0 CB A:CYS260 3.4 29.8 1.0 N A:CYS241 3.7 34.6 1.0 N A:CYS260 4.0 29.2 1.0 CA A:CYS241 4.0 41.1 1.0 CA A:CYS260 4.3 29.9 1.0 N A:CYS263 4.3 30.4 1.0 CA A:CYS263 4.3 33.0 1.0 CA A:CYS238 4.6 35.7 1.0 O A:CYS260 4.7 31.8 1.0 C A:CYS260 4.8 32.0 1.0 CB A:THR240 4.8 45.2 1.0 C A:THR240 4.8 38.1 1.0 C A:CYS241 4.8 42.8 1.0

Zinc binding site 6 out of 8 in the Structure of the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1471 b:83.5 occ:1.00 SG A:CYS352 2.1 76.5 1.0 SG A:CYS337 2.2 73.2 1.0 SG A:CYS332 2.6 68.6 1.0 CB A:CYS337 2.6 62.3 1.0 CB A:CYS332 3.6 59.4 1.0 O A:CYS337 3.7 80.3 1.0 CB A:CYS352 3.8 87.8 1.0 CA A:CYS337 3.9 68.3 1.0 C A:GLU353 4.0 77.1 1.0 N A:PHE362 4.1 1.0 1.0 N A:GLU353 4.1 89.1 1.0 C A:CYS337 4.2 71.9 1.0 CA A:GLU353 4.5 85.3 1.0 CB A:ARG334 4.5 68.6 1.0 C A:CYS352 4.6 97.0 1.0 O A:GLU353 4.6 72.3 1.0 N A:CYS337 4.8 75.1 1.0 CA A:CYS352 4.9 90.8 1.0 CB A:GLU353 4.9 79.9 1.0

Zinc binding site 7 out of 8 in the Structure of the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1472 b:53.6 occ:1.00 NE2 A:HIS373 1.9 66.9 1.0 SG A:CYS377 2.3 49.9 1.0 CB A:CYS368 2.3 44.8 1.0 SG A:CYS365 2.4 54.0 1.0 CD2 A:HIS373 2.9 61.9 1.0 CE1 A:HIS373 2.9 68.4 1.0 CB A:CYS365 3.3 51.9 1.0 SG A:CYS368 3.3 83.1 1.0 CB A:CYS377 3.4 48.9 1.0 N A:CYS368 3.4 54.9 1.0 CA A:CYS368 3.5 56.6 1.0 CA A:CYS377 3.9 51.8 1.0 ND1 A:HIS373 4.0 68.2 1.0 CG A:HIS373 4.0 66.3 1.0 N A:CYS377 4.5 55.1 1.0 C A:GLU367 4.5 56.1 1.0 C A:CYS368 4.6 56.8 1.0 NE A:ARG348 4.7 72.7 1.0 CA A:CYS365 4.7 53.5 1.0 CB A:GLU367 4.7 55.8 1.0 N A:GLU367 4.9 58.6 1.0 N A:LYS369 4.9 54.5 1.0 CA A:GLU367 4.9 52.9 1.0 C A:CYS365 4.9 54.7 1.0 NH2 A:ARG348 5.0 75.3 1.0

Zinc binding site 8 out of 8 in the Structure of the Autoinhibited Parkin Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Autoinhibited Parkin Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1473 b:31.5 occ:1.00 SG A:CYS441 2.3 27.3 1.0 SG A:CYS421 2.3 31.4 1.0 SG A:CYS418 2.3 29.5 1.0 SG A:CYS436 2.3 34.1 1.0 CB A:CYS418 3.1 33.1 1.0 CB A:CYS441 3.1 28.0 1.0 CB A:CYS421 3.2 29.0 1.0 CB A:CYS436 3.3 26.5 1.0 N A:CYS421 3.6 29.4 1.0 CA A:CYS421 4.0 31.4 1.0 CB A:LEU443 4.3 34.5 1.0 CB A:GLN438 4.4 50.0 1.0 N A:LEU443 4.5 33.3 1.0 CA A:CYS441 4.5 36.5 1.0 N A:ARG442 4.5 37.8 1.0 CA A:CYS418 4.5 31.8 1.0 CA A:CYS436 4.7 34.0 1.0 C A:CYS421 4.7 28.0 1.0 N A:HIS422 4.7 27.2 1.0 C A:ARG420 4.7 33.2 1.0 CG A:GLN438 4.7 61.2 1.0 C A:CYS441 4.8 35.0 1.0 CB A:ARG420 4.8 30.4 1.0

T.Wauer, D.Komander. Structure of the Human Parkin Ligase Domain in An Autoinhibited State. Embo J. V. 32 2099 2013.
ISSN: ISSN 0261-4189
PubMed: 23727886
DOI: 10.1038/EMBOJ.2013.125