Zinc in PDB 8wzo: Parkin in Complex with Phospho NEDD8

The structure of Parkin in Complex with Phospho NEDD8, PDB code: 8wzo 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)	40.95 / 2.25
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.976, 47.747, 127.859, 90, 105.38, 90
R / Rfree (%)	20.7 / 24.9

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

Zinc binding site 1 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:30.6 occ:1.00 ND1 A:HIS257 2.1 31.7 1.0 SG A:CYS253 2.3 29.4 1.0 SG A:CYS293 2.3 33.4 1.0 SG A:CYS289 2.3 32.1 1.0 CE1 A:HIS257 3.0 31.9 1.0 CG A:HIS257 3.1 31.4 1.0 CB A:CYS289 3.3 28.5 1.0 CB A:CYS253 3.3 30.2 1.0 CB A:CYS293 3.3 31.8 1.0 CB A:HIS257 3.5 29.6 1.0 O A:HOH639 4.0 42.9 1.0 NE2 A:HIS257 4.2 32.4 1.0 CD2 A:HIS257 4.2 31.7 1.0 CB A:ALA291 4.3 30.5 1.0 N A:HIS257 4.4 30.3 1.0 CB A:SER255 4.4 33.5 1.0 CA A:CYS293 4.6 32.6 1.0 N A:CYS293 4.6 31.8 1.0 CA A:HIS257 4.6 30.0 1.0 CA A:CYS289 4.7 27.1 1.0 CA A:CYS253 4.7 31.0 1.0 CB A:PHE251 4.9 25.3 1.0 OG A:SER255 5.0 34.6 1.0

Zinc binding site 2 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:113.6 occ:1.00 ND1 A:HIS373 2.0 121.1 1.0 SG A:CYS368 2.3 103.3 1.0 SG A:CYS365 2.3 99.3 1.0 CE1 A:HIS373 3.0 120.6 1.0 CG A:HIS373 3.1 120.0 1.0 CB A:CYS368 3.3 105.5 1.0 CB A:CYS365 3.3 95.1 1.0 CB A:HIS373 3.4 117.1 1.0 N A:CYS368 3.8 101.9 1.0 O A:CYS377 3.9 125.3 1.0 NE2 A:HIS373 4.1 120.4 1.0 CA A:CYS368 4.1 104.9 1.0 CD2 A:HIS373 4.2 121.3 1.0 CA A:CYS365 4.7 89.3 1.0 CA A:HIS373 4.7 117.0 1.0 N A:HIS373 4.7 117.3 1.0 CB A:GLU367 4.7 94.5 1.0 C A:CYS377 4.9 123.5 1.0 C A:CYS365 4.9 89.6 1.0 O A:CYS365 4.9 88.6 1.0 C A:GLU367 4.9 97.9 1.0

Zinc binding site 3 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:41.9 occ:1.00 NE2 A:HIS461 2.0 38.9 1.0 SG A:CYS446 2.3 41.0 1.0 SG A:CYS457 2.3 42.9 1.0 SG A:CYS449 2.3 49.0 1.0 CE1 A:HIS461 3.0 37.6 1.0 CD2 A:HIS461 3.1 37.2 1.0 CB A:CYS446 3.3 45.5 1.0 CB A:CYS449 3.3 49.6 1.0 CB A:CYS457 3.3 41.3 1.0 N A:CYS449 3.9 53.9 1.0 CA A:CYS457 4.1 40.6 1.0 ND1 A:HIS461 4.1 37.4 1.0 CG A:HIS461 4.2 36.3 1.0 CA A:CYS449 4.2 53.1 1.0 CB A:ASN448 4.4 53.4 1.0 ND2 A:ASN448 4.5 54.7 1.0 SG A:CYS451 4.7 58.1 1.0 CA A:CYS446 4.7 47.3 1.0 C A:ASN448 4.9 53.8 1.0 CZ3 A:TRP453 5.0 49.3 1.0

Zinc binding site 4 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:34.3 occ:1.00 SG A:CYS169 2.3 33.7 1.0 SG A:CYS196 2.3 32.1 1.0 SG A:CYS166 2.3 33.3 1.0 SG A:CYS201 2.3 37.0 1.0 CB A:CYS166 3.2 32.4 1.0 CB A:CYS196 3.3 31.6 1.0 CB A:CYS201 3.3 36.6 1.0 CB A:CYS169 3.3 36.4 1.0 N A:CYS169 3.8 38.9 1.0 OG1 A:THR173 4.1 32.8 1.0 CA A:CYS169 4.1 37.0 1.0 CB A:SER198 4.3 40.3 1.0 CB A:THR168 4.6 39.5 1.0 CA A:CYS166 4.6 32.3 1.0 CA A:CYS196 4.6 32.1 1.0 CA A:CYS201 4.7 38.2 1.0 CA A:GLY203 4.7 34.2 1.0 N A:GLY203 4.8 37.0 1.0 C A:THR168 4.8 40.7 1.0 C A:CYS169 5.0 39.0 1.0

Zinc binding site 5 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:30.3 occ:1.00 SG A:CYS263 2.3 27.6 1.0 SG A:CYS241 2.3 31.5 1.0 SG A:CYS238 2.3 28.3 1.0 SG A:CYS260 2.3 28.3 1.0 CB A:CYS238 3.2 29.4 1.0 CB A:CYS263 3.2 26.5 1.0 CB A:CYS241 3.3 32.1 1.0 CB A:CYS260 3.4 27.1 1.0 N A:CYS241 3.7 32.1 1.0 N A:CYS260 4.0 27.0 1.0 CA A:CYS241 4.0 32.5 1.0 CA A:CYS260 4.2 26.2 1.0 N A:CYS263 4.2 24.6 1.0 CA A:CYS263 4.3 25.2 1.0 CA A:CYS238 4.7 30.1 1.0 CB A:THR240 4.7 29.5 1.0 C A:THR240 4.7 31.5 1.0 C A:CYS260 4.8 25.6 1.0 C A:CYS241 4.9 33.9 1.0 O A:CYS260 4.9 25.7 1.0 N A:THR240 4.9 29.7 1.0 N A:THR242 5.0 33.8 1.0 CA A:THR240 5.0 30.2 1.0

Zinc binding site 6 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:55.2 occ:1.00 SG A:CYS332 2.3 51.4 1.0 SG A:CYS352 2.3 55.9 1.0 SG A:CYS337 2.3 57.3 1.0 SG A:CYS360 2.3 56.3 1.0 CB A:CYS352 3.2 61.9 1.0 CB A:CYS332 3.2 53.9 1.0 CB A:CYS337 3.3 57.1 1.0 CB A:CYS360 3.4 56.1 1.0 N A:CYS360 3.7 57.7 1.0 CA A:CYS360 4.1 58.6 1.0 CB A:ALA339 4.3 49.3 1.0 CB A:ARG334 4.4 67.7 1.0 CA A:CYS352 4.6 64.5 1.0 CA A:CYS332 4.7 53.3 1.0 CA A:CYS337 4.7 58.8 1.0 C A:GLY359 4.7 58.0 1.0 N A:GLY361 4.7 61.6 1.0 C A:CYS360 4.9 60.1 1.0 CB A:PHE362 4.9 66.1 1.0 N A:ALA339 4.9 50.4 1.0 CA A:GLY359 5.0 60.3 1.0

Zinc binding site 7 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:70.8 occ:1.00 SG A:CYS441 2.3 67.6 1.0 SG A:CYS436 2.3 78.2 1.0 SG A:CYS421 2.3 77.1 1.0 SG A:CYS418 2.4 66.7 1.0 CB A:CYS441 3.2 74.9 1.0 CB A:CYS436 3.2 75.8 1.0 CB A:CYS421 3.4 71.8 1.0 CB A:CYS418 3.4 65.5 1.0 N A:CYS421 3.9 70.1 1.0 CA A:CYS421 4.2 70.7 1.0 N A:ARG442 4.3 76.7 1.0 N A:LEU443 4.3 70.6 1.0 CB A:LEU443 4.5 66.9 1.0 CA A:CYS441 4.5 77.5 1.0 CB A:ARG420 4.6 76.3 1.0 C A:CYS441 4.6 77.3 1.0 CA A:CYS436 4.7 75.3 1.0 C A:ARG420 4.8 71.6 1.0 CB A:GLN438 4.8 92.4 1.0 CA A:CYS418 4.8 66.4 1.0 C A:CYS421 5.0 69.2 1.0 N A:ARG420 5.0 71.4 1.0 CA A:ARG420 5.0 73.3 1.0

Zinc binding site 8 out of 8 in the Parkin 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 Parkin in Complex with Phospho NEDD8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:27.6 occ:1.00 ND1 A:HIS215 2.2 33.3 1.0 SG A:CYS212 2.3 28.8 1.0 SG A:CYS150 2.3 24.7 1.0 SG A:CYS154 2.3 27.8 1.0 CE1 A:HIS215 3.1 34.5 1.0 CB A:CYS150 3.2 24.6 1.0 CB A:CYS212 3.2 28.7 1.0 CB A:CYS154 3.3 28.6 1.0 CG A:HIS215 3.3 34.2 1.0 CB A:HIS215 3.7 35.6 1.0 N A:CYS154 4.0 29.8 1.0 NE2 A:HIS215 4.2 37.1 1.0 CA A:CYS154 4.2 29.1 1.0 N A:HIS215 4.3 38.5 1.0 CD2 A:HIS215 4.3 36.1 1.0 CG A:GLN158 4.5 26.0 1.0 CD A:PRO153 4.6 30.6 1.0 CG A:PRO153 4.6 30.4 1.0 CA A:CYS150 4.6 24.3 1.0 CA A:CYS212 4.6 29.7 1.0 CA A:HIS215 4.7 38.6 1.0 CB A:ALA214 4.7 36.5 1.0 NE2 A:GLN158 4.9 27.7 1.0 CB A:GLN158 5.0 25.0 1.0 N A:PRO153 5.0 30.9 1.0

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