Zinc in PDB 5d0m: Structure of UBE2D2:RNF165:Ub Complex

All present enzymatic activity of Structure of UBE2D2:RNF165:Ub Complex:
6.3.2.19;

The structure of Structure of UBE2D2:RNF165:Ub Complex, PDB code: 5d0m was solved by J.D.Wright, C.L.Day, P.D.Mace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.01 / 1.91
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	62.620, 62.620, 82.250, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.3

The binding sites of Zinc atom in the Structure of UBE2D2:RNF165:Ub Complex (pdb code 5d0m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of UBE2D2:RNF165:Ub Complex, PDB code: 5d0m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:41.7 occ:1.00 ND1 C:HIS314 2.1 36.7 1.0 SG C:CYS334 2.3 46.5 1.0 SG C:CYS312 2.3 40.3 1.0 SG C:CYS331 2.3 35.3 1.0 CE1 C:HIS314 2.9 45.6 1.0 CB C:CYS331 3.1 37.4 1.0 CG C:HIS314 3.1 37.9 1.0 CB C:CYS312 3.2 40.6 1.0 CB C:CYS334 3.5 48.6 1.0 CB C:HIS314 3.5 37.4 1.0 N C:CYS334 3.8 40.7 1.0 NE2 C:HIS314 4.1 40.9 1.0 CD2 C:HIS314 4.2 41.8 1.0 CA C:CYS334 4.2 47.1 1.0 N C:HIS314 4.5 47.0 1.0 CA C:CYS312 4.5 50.4 1.0 CA C:CYS331 4.5 38.3 1.0 CA C:HIS314 4.6 41.1 1.0 CB C:ILE333 4.6 30.1 1.0 C C:CYS312 4.7 45.5 1.0 O C:CYS312 4.8 51.9 1.0 C C:ILE333 4.9 36.4 1.0 C C:CYS334 5.0 47.4 1.0

Zinc binding site 2 out of 2 in the Structure of UBE2D2:RNF165:Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of UBE2D2:RNF165:Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:54.4 occ:1.00 ND1 C:HIS317 2.1 62.0 1.0 SG C:CYS294 2.3 51.2 1.0 SG C:CYS297 2.3 60.5 1.0 SG C:CYS320 2.3 48.8 1.0 CB C:CYS294 3.0 55.7 1.0 CG C:HIS317 3.1 58.6 1.0 CE1 C:HIS317 3.1 57.7 1.0 CB C:CYS297 3.1 49.5 1.0 CB C:CYS320 3.3 57.0 1.0 CB C:HIS317 3.4 58.4 1.0 N C:CYS297 3.7 54.9 1.0 CA C:CYS297 4.0 46.1 1.0 NE2 C:HIS317 4.2 60.7 1.0 CD2 C:HIS317 4.2 62.6 1.0 N C:HIS317 4.3 51.7 1.0 CA C:CYS294 4.4 49.9 1.0 CA C:HIS317 4.4 56.6 1.0 O C:CYS294 4.6 48.4 1.0 C C:CYS294 4.7 47.6 1.0 CA C:CYS320 4.7 47.2 1.0 C C:CYS297 4.8 47.8 1.0 C C:ILE296 4.8 46.6 1.0 CB C:ILE296 4.8 40.8 1.0 N C:LEU298 4.9 44.8 1.0

J.D.Wright, P.D.Mace, C.L.Day. Secondary Ubiquitin-Ring Docking Enhances Arkadia and ARK2C E3 Ligase Activity. Nat.Struct.Mol.Biol. V. 23 45 2016.
ISSN: ESSN 1545-9985
PubMed: 26656854
DOI: 10.1038/NSMB.3142