Zinc in PDB 8wzn: PARKINK211N in Complex with Phospho NEDD8

The structure of PARKINK211N in Complex with Phospho NEDD8, PDB code: 8wzn was solved by D.R.Lenka, A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.86 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.249, 74.603, 80.067, 90, 90, 90
R / Rfree (%)	17.9 / 21.2

The binding sites of Zinc atom in the PARKINK211N in Complex with Phospho NEDD8 (pdb code 8wzn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the PARKINK211N in Complex with Phospho NEDD8, PDB code: 8wzn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:13.8 occ:1.00 ND1 A:HIS257 2.1 13.7 1.0 SG A:CYS289 2.3 14.0 1.0 SG A:CYS253 2.3 15.0 1.0 SG A:CYS293 2.4 14.8 1.0 CE1 A:HIS257 3.0 13.7 1.0 CG A:HIS257 3.1 13.7 1.0 CB A:CYS289 3.2 13.4 1.0 CB A:CYS253 3.2 14.7 1.0 CB A:CYS293 3.3 14.2 1.0 CB A:HIS257 3.5 13.6 1.0 O A:HOH692 4.0 14.4 1.0 NE2 A:HIS257 4.2 13.6 1.0 CB A:ALA291 4.2 15.6 1.0 CD2 A:HIS257 4.2 13.8 1.0 N A:HIS257 4.3 13.2 1.0 CB A:SER255 4.5 16.0 1.0 CA A:CYS293 4.5 15.6 1.0 CA A:HIS257 4.5 12.9 1.0 N A:CYS293 4.5 15.9 1.0 CA A:CYS289 4.6 13.3 1.0 CA A:CYS253 4.7 16.4 1.0 CB A:PHE251 4.9 11.1 1.0 N A:ALA291 4.9 14.9 1.0

Zinc binding site 2 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:20.7 occ:1.00 NE2 A:HIS373 2.0 18.6 1.0 SG A:CYS365 2.3 20.6 1.0 SG A:CYS377 2.3 24.5 1.0 SG A:CYS368 2.4 21.3 1.0 CE1 A:HIS373 3.0 17.8 1.0 CD2 A:HIS373 3.1 18.1 1.0 CB A:CYS365 3.1 20.2 1.0 CB A:CYS368 3.3 22.0 1.0 CB A:CYS377 3.4 24.1 1.0 N A:CYS368 3.6 26.5 1.0 CA A:CYS377 3.8 25.6 1.0 CA A:CYS368 4.1 23.7 1.0 O A:HOH847 4.1 30.5 1.0 NH1 A:ARG348 4.1 19.6 1.0 ND1 A:HIS373 4.1 17.8 1.0 CG A:HIS373 4.2 17.4 1.0 CB A:GLU367 4.3 29.3 1.0 CA A:CYS365 4.5 20.7 1.0 N A:CYS377 4.6 23.0 1.0 C A:GLU367 4.7 28.9 1.0 CA A:GLU367 4.9 29.2 1.0 C A:CYS368 4.9 24.5 1.0 N A:GLU367 4.9 27.3 1.0 C A:CYS365 5.0 21.4 1.0 N A:LYS369 5.0 23.6 1.0

Zinc binding site 3 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:15.5 occ:1.00 NE2 A:HIS461 2.1 14.6 1.0 SG A:CYS446 2.3 14.6 1.0 SG A:CYS457 2.3 15.4 1.0 SG A:CYS449 2.3 17.3 1.0 CE1 A:HIS461 3.1 14.9 1.0 CD2 A:HIS461 3.1 13.8 1.0 CB A:CYS457 3.2 13.8 1.0 CB A:CYS446 3.2 14.8 1.0 CB A:CYS449 3.2 18.9 1.0 N A:CYS449 3.9 18.2 1.0 CA A:CYS457 4.0 14.4 1.0 CA A:CYS449 4.2 19.1 1.0 O A:HOH837 4.2 22.8 1.0 ND1 A:HIS461 4.2 13.8 1.0 CG A:HIS461 4.3 13.3 1.0 CB A:ASN448 4.5 20.6 1.0 SG A:CYS451 4.6 21.8 1.0 ND2 A:ASN448 4.6 22.0 1.0 CA A:CYS446 4.6 16.0 1.0 C A:ASN448 4.9 20.3 1.0 N A:CYS457 4.9 14.1 1.0 CZ3 A:TRP453 4.9 16.2 1.0

Zinc binding site 4 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:21.0 occ:1.00 SG A:CYS169 2.3 19.7 1.0 SG A:CYS196 2.3 21.1 1.0 SG A:CYS166 2.3 20.3 1.0 SG A:CYS201 2.4 22.8 1.0 CB A:CYS166 3.1 19.9 1.0 CB A:CYS196 3.2 21.4 1.0 CB A:CYS201 3.2 21.7 1.0 CB A:CYS169 3.3 22.5 1.0 OG A:SER198 3.5 30.2 0.5 N A:CYS169 3.7 24.3 1.0 CA A:CYS169 4.0 24.2 1.0 OG1 A:THR173 4.3 22.1 1.0 CB A:THR168 4.5 26.2 1.0 CA A:GLY203 4.5 21.6 1.0 CB A:SER198 4.6 25.6 0.5 CA A:CYS166 4.6 20.2 1.0 CA A:CYS196 4.6 21.7 1.0 N A:GLY203 4.6 24.8 1.0 CA A:CYS201 4.7 22.8 1.0 C A:THR168 4.7 27.1 1.0 CB A:SER198 4.7 28.1 0.5 O A:HOH868 4.8 29.6 1.0 C A:CYS169 4.9 26.9 1.0 CA A:THR168 5.0 25.8 1.0 C A:CYS201 5.0 22.8 1.0 CG2 A:THR168 5.0 25.0 1.0

Zinc binding site 5 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:13.5 occ:1.00 SG A:CYS238 2.3 13.0 1.0 SG A:CYS260 2.3 13.6 1.0 SG A:CYS263 2.3 13.0 1.0 SG A:CYS241 2.3 14.6 1.0 CB A:CYS238 3.1 12.9 1.0 CB A:CYS263 3.1 11.6 1.0 CB A:CYS241 3.2 14.7 1.0 CB A:CYS260 3.4 12.6 1.0 N A:CYS241 3.6 15.3 1.0 NH2 A:ARG245 3.9 23.1 1.0 N A:CYS260 4.0 11.8 1.0 CA A:CYS241 4.0 15.9 1.0 OG1 A:THR240 4.0 18.1 1.0 CA A:CYS260 4.2 12.2 1.0 N A:CYS263 4.2 11.8 1.0 CA A:CYS263 4.3 12.1 1.0 CZ A:ARG245 4.5 22.6 1.0 CA A:CYS238 4.6 12.5 1.0 CD A:ARG245 4.6 21.6 1.0 C A:THR240 4.8 16.4 1.0 O A:CYS260 4.8 11.7 1.0 NE A:ARG245 4.8 21.2 1.0 C A:CYS260 4.8 12.5 1.0 C A:CYS241 4.9 15.3 1.0 N A:THR240 4.9 14.6 1.0

Zinc binding site 6 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:14.9 occ:1.00 SG A:CYS332 2.3 14.6 1.0 SG A:CYS352 2.3 16.7 1.0 SG A:CYS337 2.3 15.5 1.0 SG A:CYS360 2.4 15.2 1.0 CB A:CYS332 3.1 14.5 1.0 CB A:CYS352 3.1 14.3 1.0 CB A:CYS337 3.2 15.8 1.0 CB A:CYS360 3.3 15.3 1.0 N A:CYS360 3.8 15.9 1.0 CA A:CYS360 4.1 15.0 1.0 CB A:ALA339 4.2 15.2 1.0 CA A:CYS332 4.6 14.8 1.0 CA A:CYS352 4.6 15.0 1.0 CA A:CYS337 4.7 17.9 1.0 CB A:ARG334 4.7 19.7 1.0 C A:CYS360 4.8 15.4 1.0 C A:GLY359 4.8 16.3 1.0 CB A:PHE362 4.8 16.1 1.0 O A:HOH845 4.8 18.3 1.0 N A:GLY361 4.9 15.0 1.0 NE A:ARG334 4.9 23.2 1.0 N A:ALA339 4.9 16.3 1.0 CA A:GLY359 5.0 16.9 1.0

Zinc binding site 7 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:20.8 occ:1.00 SG A:CYS436 2.3 21.8 1.0 SG A:CYS418 2.3 18.5 1.0 SG A:CYS441 2.3 21.3 1.0 SG A:CYS421 2.3 22.1 1.0 CB A:CYS418 3.1 19.9 1.0 CB A:CYS441 3.1 22.7 1.0 CB A:CYS436 3.2 20.7 1.0 CB A:CYS421 3.2 21.7 1.0 N A:CYS421 3.6 22.3 1.0 CA A:CYS421 4.0 22.6 1.0 O A:HOH759 4.4 27.9 1.0 CA A:CYS441 4.5 23.9 1.0 N A:ARG442 4.6 22.9 1.0 CA A:CYS418 4.6 18.8 1.0 CA A:CYS436 4.6 21.2 1.0 CB A:LEU443 4.6 19.1 1.0 CB A:GLN438 4.6 32.1 1.0 CB A:ARG420 4.6 25.2 1.0 N A:LEU443 4.7 20.4 1.0 C A:ARG420 4.7 23.1 1.0 C A:CYS421 4.8 22.7 1.0 CG A:GLN438 4.8 35.1 1.0 C A:CYS441 4.8 23.1 1.0 N A:HIS422 4.9 20.8 1.0 N A:ARG420 5.0 20.3 1.0

Zinc binding site 8 out of 8 in the PARKINK211N in Complex with Phospho NEDD8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PARKINK211N in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:17.1 occ:1.00 NE2 A:HIS215 2.0 20.2 1.0 SG A:CYS154 2.3 17.7 1.0 SG A:CYS150 2.3 18.4 1.0 SG A:CYS212 2.3 15.0 1.0 CD2 A:HIS215 2.8 23.3 1.0 CE1 A:HIS215 3.0 22.8 1.0 CB A:CYS150 3.1 18.2 1.0 CB A:CYS212 3.2 16.2 1.0 CB A:CYS154 3.3 16.8 1.0 CG A:HIS215 4.0 26.1 1.0 ND1 A:HIS215 4.0 25.0 1.0 O A:HOH799 4.0 37.6 1.0 N A:CYS154 4.1 20.0 1.0 CA A:CYS154 4.3 18.6 1.0 CB A:ALA214 4.3 27.1 1.0 CG A:GLN158 4.3 15.3 1.0 CG A:PRO153 4.4 25.5 1.0 CD A:PRO153 4.5 24.3 1.0 CA A:CYS150 4.5 18.6 1.0 CA A:CYS212 4.6 16.6 1.0 NE2 A:GLN158 4.9 15.0 1.0

D.R.Lenka, A.Kumar. Parkin in Complex with Phospho NEDD8 Structure.
ISSN: ISSN 0969-2126