Zinc in PDB 5c23: Parkin (S65DUBLR0RBR)

The structure of Parkin (S65DUBLR0RBR), PDB code: 5c23 was solved by A.Kumar, J.D.Aguirre, T.E.C.Condos, R.J.Martinez-Torres, V.K.Chaugule, R.Toth, R.Sundaramoorthy, P.Mercier, A.Knebel, D.E.Spratt, K.R.Barber, G.S.Shaw, H.Walden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.16 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.279, 66.290, 205.639, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24.1

The structure of Parkin (S65DUBLR0RBR) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Parkin (S65DUBLR0RBR) (pdb code 5c23). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Parkin (S65DUBLR0RBR), PDB code: 5c23:
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 Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:36.0 occ:1.00 NE2 A:HIS215 2.0 37.7 1.0 SG A:CYS150 2.3 43.0 1.0 SG A:CYS212 2.3 32.0 1.0 SG A:CYS154 2.4 42.0 1.0 CD2 A:HIS215 2.7 38.3 1.0 CB A:CYS150 3.0 38.2 1.0 CB A:CYS212 3.1 28.3 1.0 CE1 A:HIS215 3.2 37.8 1.0 CB A:CYS154 3.3 38.1 1.0 CG A:HIS215 3.9 37.3 1.0 O A:HOH723 4.1 24.6 1.0 N A:CYS154 4.1 40.7 1.0 ND1 A:HIS215 4.1 39.0 1.0 CA A:CYS154 4.3 39.2 1.0 CD A:PRO153 4.4 45.7 1.0 CG A:GLN158 4.5 43.7 1.0 CA A:CYS150 4.5 37.8 1.0 CA A:CYS212 4.6 27.7 1.0 CB A:ALA214 4.7 31.8 1.0 N A:PRO153 4.8 44.3 1.0 O A:GLY152 4.9 47.2 1.0 CB A:GLN158 4.9 34.1 1.0 NE2 A:GLN158 4.9 46.8 1.0

Zinc binding site 2 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:43.3 occ:1.00 SG A:CYS169 2.3 39.1 1.0 SG A:CYS201 2.3 47.9 1.0 SG A:CYS196 2.3 45.2 1.0 SG A:CYS166 2.3 39.0 1.0 CB A:CYS166 3.1 33.8 1.0 CB A:CYS196 3.2 42.0 1.0 CB A:CYS169 3.4 36.4 1.0 CB A:CYS201 3.5 44.9 1.0 N A:CYS169 3.8 36.3 1.0 CA A:CYS169 4.1 36.0 1.0 OG1 A:THR173 4.4 38.2 1.0 CA A:GLY203 4.5 43.4 1.0 CA A:CYS166 4.5 32.8 1.0 CB A:THR168 4.6 46.0 1.0 CA A:CYS196 4.6 41.7 1.0 CB A:SER198 4.7 46.0 1.0 O A:HOH748 4.8 43.1 1.0 N A:GLY203 4.8 44.8 1.0 C A:THR168 4.8 40.7 1.0 CA A:CYS201 4.8 46.2 1.0 C A:CYS169 5.0 39.3 1.0

Zinc binding site 3 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:35.9 occ:1.00 SG A:CYS241 2.3 38.0 1.0 SG A:CYS260 2.3 34.1 1.0 SG A:CYS238 2.3 34.4 1.0 SG A:CYS263 2.3 34.6 1.0 CB A:CYS238 3.1 31.2 1.0 CB A:CYS263 3.1 30.2 1.0 CB A:CYS241 3.3 34.2 1.0 CB A:CYS260 3.6 30.3 1.0 N A:CYS241 3.7 33.7 1.0 OG1 A:THR240 3.9 35.2 0.5 N A:CYS260 4.0 30.4 1.0 CA A:CYS241 4.1 34.2 1.0 CA A:CYS263 4.3 29.5 1.0 CA A:CYS260 4.3 29.8 1.0 N A:CYS263 4.4 29.4 1.0 CA A:CYS238 4.6 31.6 1.0 C A:THR240 4.8 36.7 1.0 O A:CYS260 4.9 33.3 1.0 C A:CYS241 4.9 39.8 1.0 CB A:THR240 4.9 39.9 0.5 C A:CYS260 5.0 33.5 1.0 CB A:THR240 5.0 37.3 0.5 N A:THR240 5.0 32.8 1.0

Zinc binding site 4 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:46.5 occ:1.00 ND1 A:HIS257 1.9 43.4 1.0 SG A:CYS289 2.3 45.4 1.0 SG A:CYS253 2.5 42.3 1.0 SG A:CYS293 2.5 51.3 1.0 CE1 A:HIS257 2.8 43.6 1.0 CG A:HIS257 3.1 41.0 1.0 CB A:CYS253 3.2 39.5 1.0 CB A:CYS289 3.2 41.9 1.0 CB A:CYS293 3.3 47.8 1.0 CB A:HIS257 3.6 36.8 1.0 NE2 A:HIS257 4.0 43.9 1.0 CB A:ALA291 4.1 43.5 1.0 O A:HOH674 4.1 43.2 1.0 CD2 A:HIS257 4.1 43.3 1.0 N A:HIS257 4.4 36.9 1.0 CA A:HIS257 4.6 36.0 1.0 CA A:CYS293 4.6 48.1 1.0 CA A:CYS289 4.7 41.1 1.0 CA A:CYS253 4.7 39.7 1.0 CB A:SER255 4.8 44.6 1.0 N A:CYS293 4.8 47.5 1.0 CB A:PHE251 5.0 36.0 1.0

Zinc binding site 5 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:79.4 occ:1.00 SG A:CYS332 2.2 71.7 1.0 SG A:CYS337 2.6 79.4 1.0 SG A:CYS352 2.7 87.0 1.0 CB A:CYS352 3.0 84.6 1.0 CB A:CYS332 3.4 67.2 1.0 CB A:CYS337 3.5 73.6 1.0 N A:GLY361 3.9 72.6 1.0 CA A:CYS352 4.6 86.6 1.0 CA A:CYS332 4.7 66.6 1.0 CA A:CYS337 4.8 71.4 1.0 O A:CYS337 4.9 74.7 1.0 CB A:ARG334 4.9 69.9 1.0 CD1 A:PHE362 4.9 75.3 1.0

Zinc binding site 6 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:71.4 occ:1.00 SG A:CYS368 2.3 62.2 1.0 NE2 A:HIS373 2.5 70.6 1.0 SG A:CYS377 2.5 80.3 1.0 SG A:CYS365 2.5 69.8 1.0 CB A:CYS365 3.1 65.6 1.0 CE1 A:HIS373 3.2 71.7 1.0 CB A:CYS368 3.3 56.7 1.0 CD2 A:HIS373 3.5 71.6 1.0 CB A:CYS377 3.7 75.4 1.0 N A:CYS368 3.7 58.0 1.0 NH1 A:ARG348 4.0 0.5 1.0 CA A:CYS368 4.1 55.9 1.0 CA A:CYS377 4.1 76.3 1.0 ND1 A:HIS373 4.3 74.0 1.0 CG A:HIS373 4.5 71.8 1.0 CA A:CYS365 4.6 65.9 1.0 CB A:GLU367 4.7 63.9 1.0 C A:GLU367 4.8 62.1 1.0 N A:CYS377 4.9 78.0 1.0 C A:CYS368 5.0 58.5 1.0

Zinc binding site 7 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:66.7 occ:1.00 SG A:CYS436 2.2 60.3 1.0 CB A:CYS421 2.4 74.1 1.0 SG A:CYS418 2.4 67.7 1.0 SG A:CYS441 2.5 58.3 1.0 CB A:CYS441 3.0 55.7 1.0 CB A:CYS436 3.0 54.1 1.0 CB A:CYS418 3.2 65.2 1.0 SG A:CYS421 3.5 80.2 1.0 CA A:CYS421 3.5 74.4 1.0 N A:CYS421 3.6 72.6 1.0 CA A:CYS436 4.4 53.0 1.0 CA A:CYS441 4.5 55.1 1.0 C A:CYS421 4.6 79.5 1.0 CA A:CYS418 4.7 64.5 1.0 C A:ARG420 4.8 75.6 1.0 N A:ARG442 4.9 51.4 1.0 CB A:LEU443 4.9 46.2 1.0 C A:CYS441 4.9 56.1 1.0 N A:HIS422 4.9 75.1 1.0 CB A:GLN438 4.9 62.6 1.0 CG A:GLN438 4.9 79.7 1.0 N A:LEU443 5.0 47.0 1.0

Zinc binding site 8 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:43.3 occ:1.00 NE2 A:HIS461 2.1 39.8 1.0 SG A:CYS446 2.2 41.1 1.0 SG A:CYS449 2.4 43.5 1.0 SG A:CYS457 2.4 40.7 1.0 CD2 A:HIS461 3.0 39.5 1.0 CB A:CYS457 3.2 35.9 1.0 CB A:CYS449 3.2 41.2 1.0 CE1 A:HIS461 3.2 39.0 1.0 CB A:CYS446 3.3 38.3 1.0 N A:CYS449 3.8 41.6 1.0 CA A:CYS457 4.0 34.8 1.0 CA A:CYS449 4.1 41.8 1.0 CG A:HIS461 4.2 37.1 1.0 O A:HOH740 4.2 54.6 1.0 ND1 A:HIS461 4.3 38.8 1.0 CA A:CYS446 4.7 38.9 1.0 CB A:ASN448 4.8 41.9 1.0 SG A:CYS451 4.9 44.4 1.0 C A:ASN448 4.9 45.9 1.0 C A:CYS457 4.9 38.0 1.0 O A:CYS457 5.0 36.7 1.0

Zinc binding site 9 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:37.0 occ:1.00 NE2 B:HIS215 2.0 35.7 1.0 SG B:CYS150 2.2 40.6 1.0 SG B:CYS212 2.4 30.4 1.0 SG B:CYS154 2.4 42.8 1.0 CD2 B:HIS215 2.7 36.3 1.0 CB B:CYS150 3.0 36.0 1.0 CB B:CYS212 3.2 26.7 1.0 CE1 B:HIS215 3.2 35.8 1.0 CB B:CYS154 3.3 38.9 1.0 CG B:HIS215 3.9 35.2 1.0 N B:CYS154 4.1 41.4 1.0 O B:HOH736 4.2 25.3 1.0 ND1 B:HIS215 4.2 36.9 1.0 CA B:CYS154 4.3 39.9 1.0 CD B:PRO153 4.4 45.8 1.0 CA B:CYS150 4.4 36.0 1.0 CG B:GLN158 4.5 41.5 1.0 CA B:CYS212 4.6 26.2 1.0 CB B:ALA214 4.6 29.6 1.0 N B:PRO153 4.8 44.4 1.0 O B:GLY152 4.8 47.0 1.0 NE2 B:GLN158 4.9 43.7 1.0 CB B:GLN158 4.9 33.1 1.0

Zinc binding site 10 out of 16 in the Parkin (S65DUBLR0RBR)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Parkin (S65DUBLR0RBR) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:43.3 occ:1.00 SG B:CYS169 2.2 39.9 1.0 SG B:CYS201 2.3 48.8 1.0 SG B:CYS196 2.3 44.5 1.0 SG B:CYS166 2.4 37.7 1.0 CB B:CYS166 3.1 32.5 1.0 CB B:CYS196 3.2 41.2 1.0 CB B:CYS169 3.3 37.1 1.0 CB B:CYS201 3.5 45.8 1.0 N B:CYS169 3.7 36.7 1.0 CA B:CYS169 4.1 36.6 1.0 OG1 B:THR173 4.4 39.3 1.0 CA B:GLY203 4.5 44.8 1.0 CB B:THR168 4.6 43.9 1.0 CA B:CYS166 4.6 31.4 1.0 CA B:CYS196 4.6 40.8 1.0 CB B:SER198 4.6 45.1 1.0 N B:GLY203 4.7 46.3 1.0 CA B:CYS201 4.8 47.0 1.0 C B:THR168 4.8 40.4 1.0 C B:CYS169 5.0 39.8 1.0

A.Kumar, J.D.Aguirre, T.E.Condos, R.J.Martinez-Torres, V.K.Chaugule, R.Toth, R.Sundaramoorthy, P.Mercier, A.Knebel, D.E.Spratt, K.R.Barber, G.S.Shaw, H.Walden. Disruption of the Autoinhibited State Primes the E3 Ligase Parkin For Activation and Catalysis. Embo J. V. 34 2506 2015.
ISSN: ESSN 1460-2075
PubMed: 26254304
DOI: 10.15252/EMBJ.201592337