Zinc in PDB 5n2w: Wt-Parkin and Pub Complex

The structure of Wt-Parkin and Pub Complex, PDB code: 5n2w 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)	56.34 / 2.68
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	147.290, 147.290, 87.490, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 24.3

The structure of Wt-Parkin and Pub Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Wt-Parkin and Pub Complex (pdb code 5n2w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Wt-Parkin and Pub Complex, PDB code: 5n2w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:42.8 occ:1.00 ND1 A:HIS257 2.2 41.8 1.0 SG A:CYS253 2.3 44.0 1.0 SG A:CYS293 2.3 45.9 1.0 SG A:CYS289 2.3 42.5 1.0 CB A:CYS289 3.1 37.8 1.0 CG A:HIS257 3.2 40.7 1.0 CE1 A:HIS257 3.2 41.6 1.0 CB A:CYS253 3.3 40.5 1.0 CB A:CYS293 3.3 42.0 1.0 CB A:HIS257 3.4 37.6 1.0 CB A:ALA291 4.2 41.5 1.0 N A:HIS257 4.3 40.1 1.0 CD2 A:HIS257 4.3 42.1 1.0 NE2 A:HIS257 4.3 42.5 1.0 CA A:HIS257 4.5 38.4 1.0 CA A:CYS293 4.5 42.4 1.0 CA A:CYS289 4.6 36.9 1.0 N A:CYS293 4.6 41.8 1.0 CA A:CYS253 4.7 40.6 1.0 CB A:SER255 4.8 44.2 1.0 CB A:PHE251 4.9 35.7 1.0

Zinc binding site 2 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:95.1 occ:1.00 SG A:CYS368 2.3 82.8 1.0 NE2 A:HIS373 2.3 93.5 1.0 SG A:CYS365 2.4 77.3 1.0 SG A:CYS377 2.8 0.9 1.0 CE1 A:HIS373 3.2 98.5 1.0 CB A:CYS365 3.2 69.1 1.0 CB A:CYS368 3.2 80.7 1.0 CD2 A:HIS373 3.2 91.5 1.0 N A:CYS368 3.5 77.0 1.0 NH2 A:ARG348 3.8 93.2 1.0 CA A:CYS368 4.0 76.9 1.0 CB A:CYS377 4.0 0.3 1.0 ND1 A:HIS373 4.3 0.6 1.0 CG A:HIS373 4.3 93.8 1.0 NE A:ARG348 4.3 94.0 1.0 CA A:CYS377 4.4 0.9 1.0 CZ A:ARG348 4.5 0.8 1.0 CB A:GLU367 4.6 84.8 1.0 CA A:CYS365 4.6 65.0 1.0 N A:CYS377 4.7 0.4 1.0 C A:GLU367 4.7 80.2 1.0 C A:CYS368 4.9 76.7 1.0 CA A:GLU367 5.0 77.6 1.0 N A:LYS369 5.0 69.3 1.0

Zinc binding site 3 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:52.5 occ:1.00 NE2 A:HIS461 2.1 49.5 1.0 SG A:CYS449 2.2 59.7 1.0 SG A:CYS446 2.3 50.5 1.0 SG A:CYS457 2.3 47.8 1.0 CE1 A:HIS461 3.0 51.1 1.0 CD2 A:HIS461 3.2 49.0 1.0 CB A:CYS446 3.3 46.2 1.0 CB A:CYS457 3.3 43.3 1.0 CB A:CYS449 3.4 55.7 1.0 N A:CYS449 4.0 53.7 1.0 CA A:CYS457 4.0 44.5 1.0 ND1 A:HIS461 4.2 52.1 1.0 CG A:HIS461 4.3 49.1 1.0 CB A:ASN448 4.3 50.9 1.0 CA A:CYS449 4.4 55.1 1.0 SG A:CYS451 4.5 58.8 1.0 CA A:CYS446 4.7 45.4 1.0 C A:ASN448 4.8 56.8 1.0 CA A:ASN448 4.9 50.2 1.0 ND2 A:ASN448 5.0 63.4 1.0 CZ3 A:TRP453 5.0 48.6 1.0

Zinc binding site 4 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:88.1 occ:1.00 SG A:CYS196 2.2 94.7 1.0 SG A:CYS166 2.3 87.2 1.0 SG A:CYS169 2.3 92.8 1.0 SG A:CYS201 2.4 0.3 1.0 CB A:CYS166 3.0 79.4 1.0 CB A:CYS196 3.1 89.6 1.0 CB A:CYS201 3.2 0.5 1.0 CB A:CYS169 3.4 92.7 1.0 OG1 A:THR168 3.8 0.3 1.0 N A:CYS169 3.8 89.0 1.0 CA A:CYS169 4.2 90.1 1.0 OG1 A:THR173 4.3 92.6 1.0 CA A:CYS166 4.5 75.0 1.0 OG A:SER198 4.5 0.1 1.0 CA A:CYS196 4.6 88.2 1.0 CA A:CYS201 4.6 0.1 1.0 N A:GLY203 4.7 96.6 1.0 CA A:GLY203 4.7 91.5 1.0 CB A:SER198 4.7 0.9 1.0 C A:CYS201 4.9 1.0 1.0 C A:CYS166 4.9 80.1 1.0 C A:THR168 4.9 94.1 1.0 O A:CYS201 4.9 0.9 1.0 CB A:THR168 4.9 0.4 1.0

Zinc binding site 5 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:50.6 occ:1.00 SG A:CYS263 2.3 46.1 1.0 SG A:CYS238 2.3 44.1 1.0 SG A:CYS260 2.3 43.0 1.0 SG A:CYS241 2.4 52.1 1.0 CB A:CYS238 3.1 41.4 1.0 CB A:CYS263 3.2 41.1 1.0 CB A:CYS260 3.5 39.4 1.0 CB A:CYS241 3.6 48.6 1.0 N A:CYS241 3.8 46.9 1.0 N A:CYS260 3.8 38.5 1.0 O A:CYS241 3.9 59.9 1.0 NH1 A:ARG245 4.1 84.0 1.0 CA A:CYS260 4.2 38.2 1.0 CA A:CYS241 4.2 48.6 1.0 N A:CYS263 4.3 40.8 1.0 CA A:CYS263 4.4 40.1 1.0 C A:CYS241 4.5 56.9 1.0 CA A:CYS238 4.6 41.9 1.0 CZ A:ARG245 4.7 97.2 1.0 CB A:THR240 4.7 49.8 1.0 C A:CYS260 4.8 42.0 1.0 O A:CYS260 4.8 42.6 1.0 C A:THR240 4.9 49.1 1.0 N A:THR240 4.9 43.3 1.0

Zinc binding site 6 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:47.2 occ:1.00 SG A:CYS337 2.2 50.7 1.0 SG A:CYS332 2.3 44.2 1.0 SG A:CYS360 2.3 61.9 1.0 SG A:CYS352 2.4 54.4 1.0 CB A:CYS360 2.8 59.5 1.0 CB A:CYS352 3.1 51.4 1.0 CB A:CYS332 3.2 39.4 1.0 CB A:CYS337 3.3 46.7 1.0 CA A:CYS360 4.0 62.6 1.0 N A:CYS360 4.3 64.4 1.0 O A:LEU358 4.4 66.8 1.0 CB A:ARG334 4.6 44.3 1.0 CB A:ALA339 4.6 43.8 1.0 CA A:CYS352 4.6 52.0 1.0 CA A:CYS332 4.7 39.4 1.0 CA A:CYS337 4.7 47.1 1.0 N A:PHE362 4.7 52.3 1.0 CB A:PHE362 4.8 49.8 1.0 C A:CYS360 4.9 68.1 1.0 CA A:GLY361 5.0 60.0 1.0

Zinc binding site 7 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:56.6 occ:1.00 SG A:CYS436 2.3 55.5 1.0 SG A:CYS418 2.3 52.2 1.0 SG A:CYS421 2.3 55.0 1.0 SG A:CYS441 2.4 55.5 1.0 CB A:CYS441 3.0 53.7 1.0 CB A:CYS418 3.1 48.7 1.0 CB A:CYS436 3.2 50.2 1.0 CB A:CYS421 3.5 53.2 1.0 N A:CYS421 3.9 52.2 1.0 CA A:CYS421 4.3 53.2 1.0 CA A:CYS441 4.4 54.9 1.0 CB A:LEU443 4.5 45.8 1.0 CB A:GLN438 4.5 56.8 1.0 CA A:CYS418 4.5 48.6 1.0 CA A:CYS436 4.6 50.5 1.0 N A:ARG442 4.7 52.7 1.0 N A:LEU443 4.7 48.9 1.0 CB A:ARG420 4.7 52.9 1.0 C A:CYS441 4.9 57.0 1.0 C A:CYS418 5.0 54.6 1.0

Zinc binding site 8 out of 8 in the Wt-Parkin 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 Wt-Parkin and Pub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:60.0 occ:1.00 NE2 A:HIS215 2.1 69.2 1.0 SG A:CYS212 2.3 57.1 1.0 SG A:CYS150 2.3 54.9 1.0 SG A:CYS154 2.4 59.5 1.0 CD2 A:HIS215 2.6 70.7 1.0 CB A:CYS150 3.2 48.1 1.0 CB A:CYS154 3.2 54.6 1.0 CB A:CYS212 3.3 53.1 1.0 CE1 A:HIS215 3.4 70.6 1.0 CG A:HIS215 3.9 71.6 1.0 N A:CYS154 4.0 60.2 1.0 ND1 A:HIS215 4.2 73.4 1.0 CA A:CYS154 4.2 57.4 1.0 CD A:PRO153 4.3 68.0 1.0 CB A:ALA214 4.3 60.8 1.0 CG A:GLN158 4.5 53.8 1.0 O A:GLY152 4.7 68.2 1.0 N A:PRO153 4.7 66.0 1.0 CA A:CYS150 4.7 46.7 1.0 CA A:CYS212 4.7 52.3 1.0 C A:GLY152 4.9 68.5 1.0 CB A:GLN158 5.0 47.4 1.0 OE1 A:GLN158 5.0 65.7 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