Zinc in PDB 7r70: Crystal Structure of the UBARK2C Fusion Protein

All present enzymatic activity of Crystal Structure of the UBARK2C Fusion Protein:
2.3.2.27;

The structure of Crystal Structure of the UBARK2C Fusion Protein, PDB code: 7r70 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)	44.59 / 2.50
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	154.47, 154.47, 81.706, 90, 90, 120
R / Rfree (%)	20 / 24.5

The binding sites of Zinc atom in the Crystal Structure of the UBARK2C Fusion Protein (pdb code 7r70). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the UBARK2C Fusion Protein, PDB code: 7r70:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the UBARK2C Fusion Protein


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 Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:54.4 occ:1.00 ND1 A:HIS314 2.0 64.7 1.0 SG A:CYS334 2.3 52.1 1.0 SG A:CYS312 2.3 56.3 1.0 SG A:CYS331 2.3 49.1 1.0 CE1 A:HIS314 2.9 62.3 1.0 CB A:CYS331 3.0 44.5 1.0 CG A:HIS314 3.0 64.2 1.0 CB A:CYS312 3.2 48.8 1.0 CB A:CYS334 3.5 53.1 1.0 CB A:HIS314 3.5 44.2 1.0 N A:CYS334 3.8 55.6 1.0 NE2 A:HIS314 4.0 53.8 1.0 CD2 A:HIS314 4.1 61.1 1.0 CA A:CYS334 4.2 60.7 1.0 CA A:CYS331 4.5 49.8 1.0 CB A:ILE333 4.5 64.4 1.0 CA A:CYS312 4.5 60.8 1.0 N A:HIS314 4.6 50.5 1.0 CG2 A:THR9 4.6 64.5 1.0 CA A:HIS314 4.7 55.2 1.0 C A:CYS312 4.8 62.3 1.0 C A:ILE333 4.8 68.8 1.0 C A:CYS334 4.9 56.5 1.0 N A:ILE333 4.9 65.7 1.0 O A:CYS312 5.0 52.0 1.0 C A:CYS331 5.0 51.1 1.0 N A:ARG335 5.0 63.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the UBARK2C Fusion Protein


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 Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:52.2 occ:1.00 SG A:CYS320 2.2 48.1 1.0 ND1 A:HIS317 2.2 50.4 1.0 SG A:CYS297 2.3 49.9 1.0 SG A:CYS294 2.4 50.1 1.0 CB A:CYS294 3.1 45.5 1.0 CG A:HIS317 3.1 52.0 1.0 CB A:CYS297 3.3 37.3 1.0 CB A:HIS317 3.3 42.1 1.0 CB A:CYS320 3.3 48.1 1.0 CE1 A:HIS317 3.3 52.7 1.0 O1 A:GOL401 3.9 83.3 1.0 N A:CYS297 3.9 52.0 1.0 C1 A:GOL401 4.2 98.0 1.0 CA A:CYS297 4.2 52.9 1.0 CD2 A:HIS317 4.3 56.0 1.0 N A:HIS317 4.3 45.3 1.0 NE2 A:HIS317 4.3 60.8 1.0 CA A:HIS317 4.4 52.5 1.0 CA A:CYS294 4.5 48.6 1.0 CA A:CYS320 4.6 54.6 1.0 O A:CYS294 4.7 72.6 1.0 CB A:ILE296 4.8 51.9 1.0 C A:CYS294 4.9 52.0 1.0 N A:CYS320 4.9 56.2 1.0 C A:CYS297 5.0 54.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the UBARK2C Fusion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the UBARK2C Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:45.4 occ:1.00 ND1 B:HIS314 2.1 51.4 1.0 SG B:CYS334 2.3 50.4 1.0 SG B:CYS331 2.4 47.0 1.0 SG B:CYS312 2.4 47.1 1.0 CE1 B:HIS314 3.0 39.6 1.0 CB B:CYS331 3.0 38.5 1.0 CG B:HIS314 3.1 49.6 1.0 CB B:CYS312 3.4 36.6 1.0 CB B:CYS334 3.4 40.0 1.0 CB B:HIS314 3.6 40.1 1.0 N B:CYS334 3.8 48.2 1.0 NE2 B:HIS314 4.1 53.8 1.0 CA B:CYS334 4.2 41.8 1.0 CD2 B:HIS314 4.2 45.5 1.0 CG2 B:THR9 4.3 50.5 1.0 CA B:CYS331 4.5 50.8 1.0 CB B:ILE333 4.5 55.5 1.0 N B:HIS314 4.6 46.6 1.0 CA B:CYS312 4.7 46.1 1.0 CA B:HIS314 4.7 47.9 1.0 O B:CYS312 4.8 46.0 1.0 C B:CYS312 4.9 40.7 1.0 C B:ILE333 4.9 60.0 1.0 C B:CYS334 4.9 37.2 1.0 N B:ILE333 5.0 53.2 1.0 C B:CYS331 5.0 59.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the UBARK2C Fusion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the UBARK2C Fusion Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:55.4 occ:1.00 ND1 B:HIS317 2.3 50.0 1.0 SG B:CYS294 2.3 54.0 1.0 SG B:CYS297 2.4 60.9 1.0 SG B:CYS320 2.4 63.3 1.0 CB B:CYS294 2.9 47.7 1.0 CG B:HIS317 3.1 51.1 1.0 CB B:CYS297 3.1 55.7 1.0 CB B:HIS317 3.2 48.0 1.0 CB B:CYS320 3.3 54.0 1.0 CE1 B:HIS317 3.4 58.2 1.0 N B:CYS297 3.7 64.3 1.0 CA B:CYS297 4.0 61.1 1.0 N B:HIS317 4.3 60.9 1.0 CD2 B:HIS317 4.3 55.0 1.0 CA B:HIS317 4.3 56.3 1.0 CA B:CYS294 4.4 56.0 1.0 NE2 B:HIS317 4.4 67.5 1.0 O B:CYS294 4.7 66.1 1.0 CA B:CYS320 4.7 57.6 1.0 C B:CYS294 4.8 69.7 1.0 C B:CYS297 4.8 62.0 1.0 CB B:ILE296 4.8 52.4 1.0 C B:ILE296 4.9 59.8 1.0 N B:LEU298 5.0 59.2 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