Zinc in PDB 4i1f: Structure of Parkin-S223P E3 Ligase

The structure of Structure of Parkin-S223P E3 Ligase, PDB code: 4i1f was solved by J.C.Lougheed, E.Brecht, N.H.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.81 / 1.58
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	86.955, 133.155, 65.385, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.5

The structure of Structure of Parkin-S223P E3 Ligase also contains other interesting chemical elements:

Barium

(Ba)

1 atom

The binding sites of Zinc atom in the Structure of Parkin-S223P E3 Ligase (pdb code 4i1f). 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 Parkin-S223P E3 Ligase, PDB code: 4i1f:
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 Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:24.0 occ:0.70 NE2 A:HIS215 2.1 40.1 1.0 SG A:CYS212 2.2 24.4 1.0 SG A:CYS150 2.2 31.4 1.0 SG A:CYS154 2.4 35.4 1.0 CD2 A:HIS215 2.8 42.2 1.0 CB A:CYS212 3.0 20.8 1.0 CB A:CYS150 3.1 30.6 1.0 CE1 A:HIS215 3.2 42.1 1.0 CB A:CYS154 3.3 34.7 1.0 CG A:HIS215 4.1 42.6 1.0 N A:CYS154 4.1 35.2 1.0 ND1 A:HIS215 4.2 44.6 1.0 CG A:GLN158 4.3 31.1 1.0 CA A:CYS154 4.3 35.5 1.0 CD A:PRO153 4.4 48.4 1.0 CB A:ALA214 4.4 44.3 1.0 CA A:CYS212 4.6 21.5 1.0 CA A:CYS150 4.6 29.9 1.0 NE2 A:GLN158 4.6 46.5 1.0 N A:PRO153 4.9 47.1 1.0 CB A:GLN158 4.9 27.6 1.0

Zinc binding site 2 out of 8 in the Structure of Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:33.9 occ:1.00 SG A:CYS196 1.8 32.7 1.0 SG A:CYS166 2.3 28.1 1.0 SG A:CYS169 2.4 37.2 1.0 SG A:CYS201 2.4 37.5 1.0 CB A:CYS201 3.0 44.2 1.0 CB A:CYS196 3.0 33.2 1.0 CB A:CYS166 3.1 28.6 1.0 CB A:CYS169 3.2 37.1 1.0 N A:CYS169 3.7 33.8 1.0 CA A:CYS169 4.1 36.5 1.0 OG1 A:THR173 4.3 37.4 1.0 CA A:CYS196 4.4 31.4 1.0 CB A:THR168 4.4 35.9 1.0 CA A:CYS201 4.5 48.0 1.0 CA A:CYS166 4.6 29.0 1.0 CA A:GLY203 4.7 31.9 1.0 N A:GLY203 4.8 31.2 1.0 C A:THR168 4.8 34.7 1.0 OG A:SER198 4.9 55.1 1.0 C A:CYS169 4.9 38.8 1.0 CG2 A:THR168 4.9 36.7 1.0 CA A:THR168 5.0 34.1 1.0 N A:THR168 5.0 28.9 1.0

Zinc binding site 3 out of 8 in the Structure of Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:17.4 occ:1.00 SG A:CYS238 2.3 14.4 1.0 SG A:CYS263 2.3 16.9 1.0 SG A:CYS260 2.4 16.4 1.0 SG A:CYS241 2.4 20.1 1.0 CB A:CYS263 3.1 15.0 1.0 CB A:CYS238 3.2 14.2 1.0 CB A:CYS241 3.3 20.9 1.0 CB A:CYS260 3.5 17.2 1.0 N A:CYS241 3.6 19.7 1.0 O A:HOH632 3.8 37.7 1.0 CA A:CYS241 4.0 21.8 1.0 N A:CYS260 4.0 12.2 1.0 OG1 A:THR240 4.1 18.4 1.0 N A:CYS263 4.2 14.6 1.0 CA A:CYS260 4.3 15.2 1.0 CA A:CYS263 4.3 14.7 1.0 O A:HOH732 4.6 25.6 1.0 CA A:CYS238 4.7 14.5 1.0 C A:THR240 4.8 21.6 1.0 C A:CYS241 4.8 23.7 1.0 C A:CYS260 4.8 14.2 1.0 O A:CYS260 4.9 15.0 1.0 N A:THR240 5.0 17.7 1.0 N A:THR242 5.0 19.8 1.0

Zinc binding site 4 out of 8 in the Structure of Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:17.7 occ:1.00 ND1 A:HIS257 2.0 17.0 1.0 SG A:CYS289 2.3 17.8 1.0 SG A:CYS253 2.3 17.3 1.0 SG A:CYS293 2.3 18.1 1.0 CG A:HIS257 3.0 14.7 1.0 CE1 A:HIS257 3.1 15.4 1.0 CB A:CYS289 3.2 18.8 1.0 CB A:CYS253 3.2 16.6 1.0 CB A:CYS293 3.3 18.2 1.0 CB A:HIS257 3.4 13.9 1.0 O A:HOH605 4.1 18.4 1.0 CB A:ALA291 4.2 22.0 1.0 NE2 A:HIS257 4.2 16.5 1.0 CD2 A:HIS257 4.2 17.6 1.0 N A:HIS257 4.3 14.3 1.0 CB A:SER255 4.4 17.7 1.0 CA A:HIS257 4.5 11.9 1.0 N A:CYS293 4.6 20.2 1.0 CA A:CYS293 4.6 20.2 1.0 CA A:CYS289 4.7 16.2 1.0 CA A:CYS253 4.7 16.1 1.0 CB A:PHE251 4.9 14.2 1.0 N A:ALA291 4.9 17.4 1.0

Zinc binding site 5 out of 8 in the Structure of Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:26.8 occ:1.00 SG A:CYS332 2.1 26.5 1.0 SG A:CYS360 2.3 29.3 1.0 SG A:CYS337 2.3 25.2 1.0 SG A:CYS352 2.3 27.8 1.0 CB A:CYS332 3.1 18.9 1.0 CB A:CYS352 3.1 30.4 1.0 CB A:CYS337 3.2 29.4 1.0 CB A:CYS360 3.3 30.7 1.0 N A:CYS360 3.7 35.7 1.0 CA A:CYS360 4.1 32.1 1.0 CB A:ARG334 4.4 33.0 1.0 CA A:CYS332 4.5 22.1 1.0 CB A:ALA339 4.5 24.1 1.0 CA A:CYS337 4.6 28.6 1.0 CA A:CYS352 4.6 30.9 1.0 CB A:PHE362 4.7 30.8 1.0 N A:GLY338 4.8 27.6 1.0 N A:ALA339 4.8 25.7 1.0 C A:GLY359 4.8 43.7 1.0 C A:CYS360 4.8 33.0 1.0 CA A:GLY359 4.9 47.4 1.0 C A:CYS337 5.0 28.1 1.0

Zinc binding site 6 out of 8 in the Structure of Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:38.2 occ:1.00 NE2 A:HIS373 2.2 30.1 1.0 SG A:CYS377 2.3 42.0 1.0 SG A:CYS368 2.3 33.9 1.0 SG A:CYS365 2.4 34.2 1.0 CE1 A:HIS373 3.1 32.5 1.0 CB A:CYS368 3.1 33.3 1.0 CB A:CYS365 3.2 32.5 1.0 CD2 A:HIS373 3.2 31.4 1.0 CB A:CYS377 3.4 40.6 1.0 N A:CYS368 3.7 37.4 1.0 CA A:CYS377 3.9 43.9 1.0 O A:HOH863 4.0 47.8 1.0 CA A:CYS368 4.0 35.4 1.0 ND1 A:HIS373 4.3 34.3 1.0 CG A:HIS373 4.3 33.4 1.0 NH1 A:ARG348 4.4 38.7 1.0 N A:CYS377 4.5 45.6 1.0 CA A:CYS365 4.6 31.4 1.0 CB A:GLU367 4.7 42.6 1.0 C A:GLU367 4.7 43.1 1.0 C A:CYS368 4.9 31.6 1.0 O A:CYS365 4.9 32.5 1.0 N A:LYS369 5.0 29.5 1.0 C A:CYS365 5.0 34.7 1.0

Zinc binding site 7 out of 8 in the Structure of Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:28.1 occ:1.00 SG A:CYS441 2.3 29.1 1.0 SG A:CYS418 2.3 24.0 1.0 SG A:CYS421 2.4 30.7 1.0 SG A:CYS436 2.5 26.6 1.0 CB A:CYS441 2.9 26.4 1.0 CB A:CYS418 3.0 21.4 1.0 CB A:CYS436 3.2 21.3 1.0 CB A:CYS421 3.4 30.9 1.0 N A:CYS421 3.7 27.3 1.0 CA A:CYS421 4.0 30.5 1.0 CA A:CYS441 4.4 27.4 1.0 CA A:CYS418 4.5 22.2 1.0 CB A:LEU443 4.6 23.5 1.0 CA A:CYS436 4.6 20.8 1.0 CB A:GLN438 4.7 28.9 1.0 C A:ARG420 4.7 27.7 1.0 C A:CYS421 4.7 32.7 1.0 CG A:GLN438 4.8 38.1 1.0 CG A:ARG420 4.8 35.5 1.0 N A:LEU443 4.8 23.6 1.0 N A:ARG442 4.8 26.9 1.0 CB A:ARG420 4.8 26.9 1.0 C A:CYS441 4.8 25.9 1.0 N A:ARG420 4.9 26.7 1.0 N A:HIS422 4.9 26.9 1.0 CD A:ARG420 5.0 34.5 1.0

Zinc binding site 8 out of 8 in the Structure of Parkin-S223P E3 Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Parkin-S223P E3 Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:15.9 occ:1.00 NE2 A:HIS461 2.0 13.5 1.0 SG A:CYS446 2.3 14.7 1.0 SG A:CYS457 2.3 17.5 1.0 SG A:CYS449 2.4 17.1 1.0 CE1 A:HIS461 2.9 13.1 1.0 CD2 A:HIS461 3.1 14.2 1.0 CB A:CYS449 3.1 16.0 1.0 CB A:CYS457 3.2 17.9 1.0 CB A:CYS446 3.2 12.9 1.0 O A:HOH858 3.5 17.5 1.0 N A:CYS449 3.8 17.5 1.0 CA A:CYS457 4.0 15.5 1.0 ND1 A:HIS461 4.1 13.4 1.0 CA A:CYS449 4.1 18.9 1.0 CG A:HIS461 4.2 12.4 1.0 CB A:ASN448 4.4 18.3 1.0 CA A:CYS446 4.6 13.1 1.0 ND2 A:ASN448 4.8 19.7 1.0 C A:ASN448 4.8 16.1 1.0 CZ3 A:TRP453 4.9 14.3 1.0 N A:ASN448 4.9 15.2 1.0 CA A:ASN448 5.0 16.5 1.0 N A:CYS457 5.0 14.8 1.0

B.E.Riley, J.C.Lougheed, K.Callaway, M.Velasquez, E.Brecht, L.Nguyen, T.Shaler, D.Walker, Y.Yang, K.Regnstrom, L.Diep, Z.Zhang, S.Chiou, M.Bova, D.R.Artis, N.Yao, J.Baker, T.Yednock, J.A.Johnston. Structure and Function of Parkin E3 Ubiquitin Ligase Reveals Aspects of Ring and Hect Ligases. Nat Commun V. 4 1982 2013.
ISSN: ESSN 2041-1723
PubMed: 23770887
DOI: 10.1038/NCOMMS2982