Zinc in PDB 7r71: Crystal Structure of the UBARK2C-UBCH5B~Ub Complex

All present enzymatic activity of Crystal Structure of the UBARK2C-UBCH5B~Ub Complex:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The structure of Crystal Structure of the UBARK2C-UBCH5B~Ub Complex, PDB code: 7r71 was solved by A.Paluda, A.J.Middleton, P.D.Mace, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.59 / 2.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.33, 75.668, 99.379, 90, 90, 90
R / Rfree (%)	22.6 / 27.1

The binding sites of Zinc atom in the Crystal Structure of the UBARK2C-UBCH5B~Ub Complex (pdb code 7r71). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the UBARK2C-UBCH5B~Ub Complex, PDB code: 7r71:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the UBARK2C-UBCH5B~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the UBARK2C-UBCH5B~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:48.9 occ:1.00 ND1 A:HIS314 2.2 64.8 1.0 SG A:CYS334 2.3 64.2 1.0 SG A:CYS331 2.3 59.5 1.0 SG A:CYS312 2.4 51.7 1.0 CE1 A:HIS314 2.9 60.6 1.0 CB A:CYS312 3.2 51.0 1.0 CB A:CYS331 3.2 58.2 1.0 CG A:HIS314 3.2 56.8 1.0 CB A:CYS334 3.5 57.6 1.0 N A:CYS334 3.7 61.5 1.0 CB A:HIS314 3.7 57.4 1.0 NE2 A:HIS314 4.0 51.0 1.0 CD2 A:HIS314 4.2 52.7 1.0 CA A:CYS334 4.2 63.5 1.0 CB A:ILE333 4.3 41.5 1.0 C A:ILE333 4.6 56.5 1.0 CA A:CYS312 4.6 44.6 1.0 CA A:CYS331 4.6 50.9 1.0 CG2 A:THR9 4.7 57.6 1.0 N A:ILE333 4.7 54.0 1.0 CA A:ILE333 4.7 53.2 1.0 O A:CYS312 4.8 63.1 1.0 C A:CYS312 4.8 47.8 1.0 C A:CYS334 4.9 63.6 1.0 C A:CYS331 4.9 48.3 1.0 O D:GLY35 5.0 71.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the UBARK2C-UBCH5B~Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the UBARK2C-UBCH5B~Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:59.6 occ:1.00 ND1 A:HIS317 2.3 92.8 1.0 SG A:CYS294 2.4 48.2 1.0 SG A:CYS320 2.4 63.1 1.0 SG A:CYS297 2.4 85.5 1.0 CB A:CYS294 2.9 48.9 1.0 CB A:CYS297 3.1 75.1 1.0 CG A:HIS317 3.1 92.1 1.0 CB A:CYS320 3.2 54.3 1.0 CB A:HIS317 3.3 79.6 1.0 CE1 A:HIS317 3.4 95.1 1.0 N A:CYS297 3.7 79.3 1.0 CA A:CYS297 4.0 74.9 1.0 N A:HIS317 4.2 55.4 1.0 CD2 A:HIS317 4.3 94.2 1.0 CA A:CYS294 4.4 58.5 1.0 CA A:HIS317 4.4 73.1 1.0 NE2 A:HIS317 4.4 96.8 1.0 CA A:CYS320 4.7 62.6 1.0 O A:CYS294 4.7 55.8 1.0 CB A:ILE296 4.7 55.2 1.0 C A:ILE296 4.8 74.9 1.0 C A:CYS294 4.8 61.6 1.0 C A:CYS297 4.8 70.0 1.0 OG A:SER299 4.9 72.5 1.0 N A:CYS320 5.0 76.1 1.0 N A:LEU298 5.0 68.1 1.0

A.Paluda, A.J.Middleton, C.Rossig, P.D.Mace, C.L.Day. Ubiquitin and A Charged Loop Regulate the Ubiquitin E3 Ligase Activity of ARK2C. Nat Commun V. 13 1181 2022.
ISSN: ESSN 2041-1723
PubMed: 35246518
DOI: 10.1038/S41467-022-28782-Y