Zinc in PDB 4v3l: RNF38-Ub-UBCH5B-Ub Complex

All present enzymatic activity of RNF38-Ub-UBCH5B-Ub Complex:
6.3.2.19;

The structure of RNF38-Ub-UBCH5B-Ub Complex, PDB code: 4v3l was solved by L.Buetow, M.Gabrielsen, N.G.Anthony, H.Dou, A.Patel, H.Aitkenhead, G.J.Sibbet, B.O.Smith, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.687 / 1.53
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.840, 62.840, 191.060, 90.00, 90.00, 120.00
R / Rfree (%)	18.28 / 19.26

The binding sites of Zinc atom in the RNF38-Ub-UBCH5B-Ub Complex (pdb code 4v3l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the RNF38-Ub-UBCH5B-Ub Complex, PDB code: 4v3l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the RNF38-Ub-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 RNF38-Ub-UBCH5B-Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1463 b:17.5 occ:1.00 ND1 C:HIS436 2.1 16.3 1.0 SG C:CYS439 2.3 19.4 1.0 SG C:CYS416 2.3 19.5 1.0 SG C:CYS413 2.3 16.4 1.0 CE1 C:HIS436 3.1 20.1 1.0 CB C:CYS413 3.1 17.0 1.0 CG C:HIS436 3.1 18.2 1.0 CB C:CYS439 3.3 19.4 1.0 CB C:CYS416 3.3 18.7 1.0 CB C:HIS436 3.4 15.4 1.0 N C:CYS416 3.7 17.9 1.0 CA C:CYS416 4.1 18.5 1.0 O C:HOH2027 4.2 33.8 1.0 NE2 C:HIS436 4.2 22.3 1.0 CD2 C:HIS436 4.2 20.5 1.0 N C:HIS436 4.3 16.1 1.0 O C:HOH2004 4.4 57.1 1.0 CA C:HIS436 4.4 17.0 1.0 CA C:CYS413 4.5 16.7 1.0 O C:CYS413 4.6 17.7 1.0 CA C:CYS439 4.7 16.5 1.0 CB C:VAL415 4.7 18.4 1.0 C C:CYS413 4.8 16.4 1.0 C C:VAL415 4.8 17.8 1.0 O C:HOH2050 4.9 30.4 1.0 N C:CYS439 5.0 17.8 1.0

Zinc binding site 2 out of 2 in the RNF38-Ub-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 RNF38-Ub-UBCH5B-Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1464 b:17.1 occ:1.00 ND1 C:HIS433 2.1 18.7 1.0 SG C:CYS453 2.3 17.3 1.0 SG C:CYS431 2.3 18.2 1.0 SG C:CYS450 2.3 15.7 1.0 CE1 C:HIS433 3.0 21.8 1.0 CG C:HIS433 3.1 18.5 1.0 CB C:CYS450 3.1 16.2 1.0 CB C:CYS431 3.3 20.1 1.0 CB C:HIS433 3.5 19.1 1.0 CB C:CYS453 3.5 17.0 1.0 N C:CYS453 3.7 13.6 1.0 CA C:CYS453 4.1 15.6 1.0 NE2 C:HIS433 4.1 19.6 1.0 CD2 C:HIS433 4.2 20.5 1.0 N C:HIS433 4.5 18.3 1.0 CB C:ILE452 4.5 15.8 1.0 CA C:CYS450 4.6 13.4 1.0 CA C:CYS431 4.6 21.1 1.0 CA C:HIS433 4.6 16.9 1.0 O C:CYS431 4.7 22.1 1.0 C C:ILE452 4.7 15.0 1.0 C C:CYS431 4.7 23.7 1.0 CB C:ALA455 4.7 21.6 1.0 O C:HOH2044 4.8 21.9 1.0 C C:CYS453 4.8 15.3 1.0 CA C:ILE452 4.9 15.0 1.0 N C:ILE452 4.9 14.8 1.0 N C:ARG454 4.9 15.1 1.0 O C:HOH2062 5.0 21.8 1.0 CG2 C:ILE452 5.0 17.9 1.0 N C:ALA455 5.0 17.1 1.0

L.Buetow, M.Gabrielsen, N.G.Anthony, H.Dou, A.Patel, H.Aitkenhead, G.J.Sibbet, B.O.Smith, D.T.Huang. Activation of A Primed Ring E3-E2-Ubiquitin Complex By Non- Covalent Ubiquitin. Mol.Cell 2015.
ISSN: ESSN 1097-4164
PubMed: 25801170
DOI: 10.1016/J.MOLCEL.2015.02.017