Zinc in PDB 5n38: S65DPARKIN and Pub Complex

The structure of S65DPARKIN and Pub Complex, PDB code: 5n38 was solved by A.Kumar, V.K.Chaugule, C.Johnson, R.Toth, R.Sundaramoorthy, A.Knebel, H.Walden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.56 / 2.60
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	146.540, 146.540, 88.440, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 23.6

The structure of S65DPARKIN and Pub Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the S65DPARKIN and Pub Complex (pdb code 5n38). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the S65DPARKIN and Pub Complex, PDB code: 5n38:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2503 b:42.4 occ:1.00 SG A:CYS260 2.3 36.6 1.0 SG A:CYS263 2.3 44.3 1.0 SG A:CYS238 2.3 38.8 1.0 SG A:CYS241 2.4 41.8 1.0 CB A:CYS238 3.1 35.7 1.0 CB A:CYS263 3.2 39.5 1.0 CB A:CYS241 3.3 38.5 1.0 CB A:CYS260 3.5 33.6 1.0 N A:CYS241 3.8 39.0 1.0 N A:CYS260 4.0 33.4 1.0 CA A:CYS241 4.1 38.9 1.0 NH1 A:ARG245 4.1 70.0 1.0 CA A:CYS260 4.3 33.4 1.0 N A:CYS263 4.3 38.9 1.0 CA A:CYS263 4.4 38.5 1.0 CZ A:ARG245 4.5 88.4 1.0 CA A:CYS238 4.6 35.5 1.0 O A:CYS260 4.7 36.5 1.0 CB A:THR240 4.8 42.3 1.0 NH2 A:ARG245 4.8 74.0 1.0 C A:CYS260 4.8 37.8 1.0 C A:THR240 4.9 42.4 1.0 C A:CYS241 4.9 44.1 1.0

Zinc binding site 2 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2504 b:41.4 occ:1.00 ND1 A:HIS257 2.1 42.8 1.0 SG A:CYS289 2.3 35.4 1.0 SG A:CYS253 2.3 40.7 1.0 SG A:CYS293 2.4 35.9 1.0 CB A:CYS289 3.1 30.7 1.0 CG A:HIS257 3.1 41.1 1.0 CB A:CYS253 3.1 37.4 1.0 CE1 A:HIS257 3.2 43.2 1.0 CB A:HIS257 3.4 37.3 1.0 CB A:CYS293 3.5 31.9 1.0 CB A:ALA291 4.1 35.8 1.0 CD2 A:HIS257 4.3 43.7 1.0 NE2 A:HIS257 4.3 44.0 1.0 N A:HIS257 4.4 38.0 1.0 O A:HOH2634 4.4 41.2 1.0 CA A:HIS257 4.5 36.5 1.0 CA A:CYS289 4.5 29.4 1.0 CA A:CYS253 4.6 37.9 1.0 CA A:CYS293 4.7 32.8 1.0 N A:CYS293 4.7 33.7 1.0 CB A:SER255 4.8 40.5 1.0 CB A:PHE251 4.8 33.8 1.0

Zinc binding site 3 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2505 b:85.5 occ:1.00 NE2 A:HIS373 2.1 94.0 1.0 SG A:CYS365 2.2 65.2 1.0 SG A:CYS368 2.2 75.3 1.0 SG A:CYS377 2.5 0.0 1.0 CB A:CYS365 2.9 58.7 1.0 CE1 A:HIS373 2.9 96.5 1.0 CB A:CYS368 3.1 71.8 1.0 CD2 A:HIS373 3.2 93.2 1.0 N A:CYS368 3.3 68.6 1.0 CA A:CYS368 3.8 69.4 1.0 CB A:CYS377 3.8 98.9 1.0 ND1 A:HIS373 4.1 97.8 1.0 CG A:HIS373 4.2 93.4 1.0 CA A:CYS365 4.3 55.8 1.0 CB A:GLU367 4.4 71.6 1.0 CA A:CYS377 4.4 0.5 1.0 NE A:ARG348 4.4 0.0 1.0 C A:GLU367 4.5 70.3 1.0 N A:CYS377 4.6 91.2 1.0 C A:CYS368 4.6 72.6 1.0 NH2 A:ARG348 4.6 0.3 1.0 N A:LYS369 4.7 68.0 1.0 CA A:GLU367 4.8 67.3 1.0 C A:CYS365 4.8 61.8 1.0 N A:GLU367 4.9 65.8 1.0

Zinc binding site 4 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2506 b:41.3 occ:1.00 SG A:CYS332 2.2 40.8 1.0 SG A:CYS337 2.3 41.5 1.0 SG A:CYS352 2.3 51.7 1.0 CB A:CYS360 2.4 54.2 1.0 SG A:CYS360 2.7 56.9 1.0 CB A:CYS332 3.0 36.8 1.0 CB A:CYS352 3.2 47.7 1.0 CB A:CYS337 3.3 37.2 1.0 CA A:CYS360 3.8 56.2 1.0 N A:CYS360 4.3 58.1 1.0 CA A:CYS332 4.4 35.7 1.0 O A:LEU358 4.4 62.5 1.0 CB A:ALA339 4.6 36.4 1.0 CA A:CYS352 4.6 48.9 1.0 CB A:PHE362 4.7 46.1 1.0 CB A:ARG334 4.7 33.6 1.0 CA A:CYS337 4.7 37.8 1.0 N A:PHE362 4.8 48.9 1.0 O A:CYS352 4.8 59.0 1.0 C A:CYS360 4.9 60.0 1.0 C A:GLY359 5.0 66.4 1.0

Zinc binding site 5 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2507 b:46.6 occ:1.00 SG A:CYS446 2.1 40.2 1.0 SG A:CYS457 2.2 49.9 1.0 SG A:CYS449 2.3 42.4 1.0 NE2 A:HIS461 2.3 37.4 1.0 CB A:CYS449 3.1 38.2 1.0 CB A:CYS446 3.2 35.2 1.0 CE1 A:HIS461 3.2 38.6 1.0 CB A:CYS457 3.3 45.8 1.0 CD2 A:HIS461 3.3 38.0 1.0 N A:CYS449 3.8 38.8 1.0 CA A:CYS449 4.1 38.3 1.0 CA A:CYS457 4.1 47.1 1.0 CB A:ASN448 4.2 37.0 1.0 ND1 A:HIS461 4.4 40.8 1.0 SG A:CYS451 4.4 44.3 1.0 CG A:HIS461 4.4 38.9 1.0 CA A:CYS446 4.6 33.7 1.0 OD1 A:ASN448 4.7 52.7 1.0 C A:ASN448 4.7 43.0 1.0 CG A:ASN448 4.9 59.9 1.0 CA A:ASN448 4.9 38.4 1.0 CZ3 A:TRP453 5.0 44.4 1.0

Zinc binding site 6 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2508 b:45.1 occ:1.00 SG A:CYS421 2.3 41.9 1.0 SG A:CYS436 2.4 40.8 1.0 SG A:CYS418 2.4 40.5 1.0 SG A:CYS441 2.5 39.6 1.0 CB A:CYS418 3.1 35.9 1.0 CB A:CYS441 3.1 35.8 1.0 CB A:CYS436 3.2 38.0 1.0 CB A:CYS421 3.5 39.0 1.0 N A:CYS421 3.8 39.1 1.0 CA A:CYS421 4.2 39.1 1.0 CB A:LEU443 4.4 36.5 1.0 CB A:GLN438 4.5 40.8 1.0 CA A:CYS441 4.5 37.2 1.0 CA A:CYS418 4.5 35.6 1.0 CG A:GLN438 4.6 38.1 1.0 CA A:CYS436 4.7 38.4 1.0 N A:ARG442 4.7 39.1 1.0 CB A:ARG420 4.7 34.0 1.0 N A:LEU443 4.8 38.1 1.0 C A:ARG420 4.9 42.5 1.0

Zinc binding site 7 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2509 b:93.5 occ:1.00 SG A:CYS166 2.4 88.4 1.0 SG A:CYS201 2.5 0.9 1.0 SG A:CYS196 2.6 0.6 1.0 SG A:CYS169 2.6 99.5 1.0 CB A:CYS166 3.0 82.2 1.0 CB A:CYS169 3.1 98.0 1.0 N A:CYS169 3.1 94.5 1.0 CB A:CYS196 3.4 0.1 1.0 CA A:CYS169 3.6 95.3 1.0 CB A:CYS201 3.8 0.0 1.0 CB A:THR168 4.0 0.2 1.0 C A:THR168 4.2 97.4 1.0 OG1 A:THR173 4.2 0.6 1.0 CA A:GLY203 4.4 0.2 1.0 OG A:SER198 4.4 0.4 1.0 CA A:THR168 4.5 92.5 1.0 CA A:CYS166 4.5 79.1 1.0 C A:CYS169 4.6 95.0 1.0 N A:THR168 4.7 89.7 1.0 N A:GLY203 4.7 0.5 1.0 N A:ARG170 4.7 88.6 1.0 CG2 A:THR168 4.8 0.3 1.0 OG1 A:THR168 4.8 99.9 1.0 CA A:CYS196 4.8 0.0 1.0

Zinc binding site 8 out of 8 in the S65DPARKIN and Pub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of S65DPARKIN and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2510 b:56.0 occ:1.00 NE2 A:HIS215 2.1 70.7 1.0 SG A:CYS150 2.3 49.3 1.0 SG A:CYS154 2.3 52.4 1.0 SG A:CYS212 2.3 52.6 1.0 CD2 A:HIS215 2.5 71.1 1.0 CB A:CYS150 3.2 43.5 1.0 CB A:CYS212 3.2 49.1 1.0 CB A:CYS154 3.4 48.8 1.0 CE1 A:HIS215 3.4 71.2 1.0 CG A:HIS215 3.8 69.9 1.0 N A:CYS154 4.1 53.2 1.0 ND1 A:HIS215 4.2 72.4 1.0 CA A:CYS154 4.4 51.1 1.0 CB A:ALA214 4.5 54.2 1.0 CD A:PRO153 4.5 58.5 1.0 CA A:CYS150 4.6 42.6 1.0 CG A:GLN158 4.6 52.8 1.0 CA A:CYS212 4.6 48.9 1.0 CG A:PRO153 4.7 63.5 1.0 N A:PRO153 4.8 56.9 1.0 O A:GLY152 4.9 61.2 1.0

A.Kumar, V.K.Chaugule, T.E.C.Condos, K.R.Barber, C.Johnson, R.Toth, R.Sundaramoorthy, A.Knebel, G.S.Shaw, H.Walden. Parkin-Phosphoubiquitin Complex Reveals Cryptic Ubiquitin-Binding Site Required For Rbr Ligase Activity. Nat. Struct. Mol. Biol. V. 24 475 2017.
ISSN: ESSN 1545-9985
PubMed: 28414322
DOI: 10.1038/NSMB.3400