Zinc in PDB 7ojx: E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis

All present enzymatic activity of E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis:
2.3.2.23; 2.3.2.27;

The structure of E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis, PDB code: 7ojx was solved by K.A.Majorek, M.A.Nakasone, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.34 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.835, 85.835, 167.354, 90, 90, 120
R / Rfree (%)	18.8 / 23.6

The binding sites of Zinc atom in the E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis (pdb code 7ojx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis, PDB code: 7ojx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:63.8 occ:1.00 SG A:CYS439 2.2 73.5 1.0 ND1 A:HIS436 2.2 71.6 1.0 SG A:CYS413 2.3 75.6 1.0 SG A:CYS416 2.4 82.3 1.0 CG A:HIS436 3.1 69.8 1.0 CB A:CYS413 3.1 68.6 1.0 CB A:HIS436 3.2 57.4 1.0 CB A:CYS439 3.3 64.8 1.0 CB A:CYS416 3.3 75.0 1.0 CE1 A:HIS436 3.3 68.9 1.0 N A:CYS416 3.6 70.8 1.0 CA A:CYS416 4.0 75.3 1.0 CD2 A:HIS436 4.3 71.2 1.0 NE2 A:HIS436 4.4 74.2 1.0 N A:HIS436 4.4 66.3 1.0 CA A:HIS436 4.4 62.7 1.0 O A:CYS413 4.5 70.4 1.0 CA A:CYS413 4.5 72.0 1.0 CB A:VAL415 4.5 65.2 1.0 CA A:CYS439 4.6 72.4 1.0 C A:VAL415 4.6 72.8 1.0 C A:CYS413 4.7 68.0 1.0 N A:CYS439 4.9 70.1 1.0 N A:VAL415 4.9 72.0 1.0 CA A:VAL415 4.9 68.7 1.0 C A:CYS416 4.9 69.9 1.0

Zinc binding site 2 out of 2 in the E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E2 UBE2K Covalently Linked to Donor Ub, Acceptor Di-Ub, and Ring E3 Primed For K48-Linked Ub Chain Synthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:72.1 occ:1.00 ND1 A:HIS433 1.8 88.0 1.0 SG A:CYS450 2.3 66.9 1.0 SG A:CYS431 2.3 73.2 1.0 SG A:CYS453 2.4 76.2 1.0 CE1 A:HIS433 2.6 79.6 1.0 CG A:HIS433 3.0 85.2 1.0 CB A:CYS450 3.2 76.7 1.0 CB A:CYS431 3.2 73.0 1.0 CB A:CYS453 3.4 68.6 1.0 CB A:HIS433 3.5 72.3 1.0 N A:CYS453 3.8 73.5 1.0 NE2 A:HIS433 3.8 83.9 1.0 CD2 A:HIS433 4.0 81.1 1.0 CA A:CYS453 4.1 72.9 1.0 CB A:ILE452 4.5 71.1 1.0 CA A:CYS431 4.5 84.9 1.0 N A:HIS433 4.5 74.8 1.0 O A:CYS431 4.5 84.5 1.0 CA A:CYS450 4.6 71.0 1.0 CA A:HIS433 4.6 69.5 1.0 C A:CYS431 4.7 84.6 1.0 CG2 A:ILE452 4.7 61.1 1.0 C A:CYS453 4.7 72.7 1.0 CB A:ALA455 4.8 66.3 1.0 C A:ILE452 4.8 75.0 1.0 N A:ARG454 4.8 62.4 1.0 N A:ILE452 4.9 64.4 1.0 C A:CYS450 4.9 73.0 1.0 N A:ALA455 4.9 75.3 1.0 CA A:ILE452 5.0 68.6 1.0

M.A.Nakasone, K.A.Majorek, M.Gabrielsen, G.J.Sibbet, B.O.Smith, D.T.Huang. Structure of UBE2K-Ub/E3/Polyub Reveals Mechanisms of K48-Linked Ub Chain Extension. Nat.Chem.Biol. V. 18 422 2022.
ISSN: ESSN 1552-4469
PubMed: 35027744
DOI: 10.1038/S41589-021-00952-X