Zinc in PDB 4v3k: RNF38-UBCH5B-Ub Complex

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

The structure of RNF38-UBCH5B-Ub Complex, PDB code: 4v3k 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)	34.905 / 2.04
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	139.620, 139.620, 70.690, 90.00, 90.00, 90.00
R / Rfree (%)	18.07 / 22.34

The structure of RNF38-UBCH5B-Ub Complex also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Zinc atom in the RNF38-UBCH5B-Ub Complex (pdb code 4v3k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RNF38-UBCH5B-Ub Complex, PDB code: 4v3k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RNF38-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-UBCH5B-Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1465 b:23.5 occ:1.00 ND1 C:HIS436 2.1 20.3 1.0 SG C:CYS439 2.3 25.0 1.0 SG C:CYS413 2.4 18.9 1.0 SG C:CYS416 2.4 21.4 1.0 CB C:CYS413 3.0 15.9 1.0 CG C:HIS436 3.0 18.4 1.0 CE1 C:HIS436 3.1 24.5 1.0 CB C:HIS436 3.2 20.4 1.0 CB C:CYS439 3.3 21.7 1.0 CB C:CYS416 3.3 20.4 1.0 N C:CYS416 3.8 18.5 1.0 O C:HOH2016 3.9 33.5 1.0 CA C:CYS416 4.1 21.9 1.0 CD2 C:HIS436 4.2 19.7 1.0 NE2 C:HIS436 4.2 21.2 1.0 CA C:HIS436 4.4 19.9 1.0 N C:HIS436 4.4 20.4 1.0 CA C:CYS413 4.4 20.2 1.0 CA C:CYS439 4.6 25.6 1.0 CB C:VAL415 4.7 21.8 1.0 O C:CYS413 4.7 17.6 1.0 C C:CYS413 4.8 21.8 1.0 C C:VAL415 4.9 18.4 1.0 N C:CYS439 4.9 22.9 1.0

Zinc binding site 2 out of 4 in the RNF38-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-UBCH5B-Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1466 b:18.3 occ:1.00 ND1 C:HIS433 2.1 16.8 1.0 SG C:CYS453 2.3 18.5 1.0 SG C:CYS431 2.3 17.3 1.0 SG C:CYS450 2.4 19.2 1.0 CE1 C:HIS433 3.0 19.1 1.0 CB C:CYS450 3.1 16.9 1.0 CG C:HIS433 3.1 17.1 1.0 CB C:CYS431 3.2 18.4 1.0 CB C:CYS453 3.5 22.4 1.0 CB C:HIS433 3.5 15.2 1.0 N C:CYS453 3.6 18.7 1.0 CA C:CYS453 4.1 19.2 1.0 NE2 C:HIS433 4.1 21.6 1.0 CD2 C:HIS433 4.2 15.7 1.0 N C:HIS433 4.5 19.0 1.0 CA C:CYS431 4.5 18.4 1.0 CB C:ALA455 4.5 20.6 1.0 CA C:CYS450 4.6 22.6 1.0 CB C:ILE452 4.6 16.3 1.0 CA C:HIS433 4.6 18.9 1.0 O C:CYS431 4.7 22.4 1.0 C C:CYS431 4.7 19.3 1.0 C C:ILE452 4.7 21.7 1.0 O C:HOH2026 4.7 21.2 1.0 C C:CYS453 4.8 19.3 1.0 N C:ALA455 4.9 19.4 1.0 CG2 C:ILE452 4.9 17.1 1.0 N C:ARG454 4.9 16.0 1.0 CA C:ILE452 5.0 14.1 1.0

Zinc binding site 3 out of 4 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RNF38-UBCH5B-Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1460 b:25.1 occ:1.00 ND1 F:HIS436 2.2 23.1 1.0 SG F:CYS439 2.3 24.3 1.0 SG F:CYS416 2.4 22.8 1.0 SG F:CYS413 2.4 22.6 1.0 CG F:HIS436 3.0 23.7 1.0 CB F:CYS413 3.1 19.1 1.0 CB F:HIS436 3.2 21.6 1.0 CB F:CYS439 3.2 17.7 1.0 CE1 F:HIS436 3.3 27.9 1.0 CB F:CYS416 3.3 20.1 1.0 N F:CYS416 3.7 20.8 1.0 CA F:CYS416 4.1 23.6 1.0 CD2 F:HIS436 4.2 28.5 1.0 N F:HIS436 4.3 25.0 1.0 NE2 F:HIS436 4.3 30.5 1.0 CA F:HIS436 4.4 23.4 1.0 O F:HOH2010 4.4 36.6 1.0 CA F:CYS413 4.5 24.7 1.0 CA F:CYS439 4.6 25.1 1.0 O F:HOH2001 4.6 37.7 1.0 CB F:VAL415 4.7 24.5 1.0 O F:CYS413 4.8 25.9 1.0 C F:VAL415 4.8 21.7 1.0 C F:CYS413 4.8 22.3 1.0 N F:CYS439 4.9 28.4 1.0 C F:CYS416 5.0 26.5 1.0

Zinc binding site 4 out of 4 in the RNF38-UBCH5B-Ub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RNF38-UBCH5B-Ub Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1461 b:21.2 occ:1.00 ND1 F:HIS433 2.1 21.6 1.0 SG F:CYS453 2.3 19.0 1.0 SG F:CYS450 2.3 17.4 1.0 SG F:CYS431 2.4 17.3 1.0 CE1 F:HIS433 3.0 20.4 1.0 CB F:CYS450 3.1 19.9 1.0 CG F:HIS433 3.1 21.4 1.0 CB F:CYS431 3.2 24.5 1.0 CB F:CYS453 3.5 24.6 1.0 CB F:HIS433 3.5 15.4 1.0 N F:CYS453 3.6 19.8 1.0 CA F:CYS453 4.0 21.3 1.0 NE2 F:HIS433 4.2 18.4 1.0 CD2 F:HIS433 4.2 19.5 1.0 N F:HIS433 4.5 21.5 1.0 CB F:ILE452 4.5 17.2 1.0 CA F:CYS431 4.6 25.2 1.0 CA F:CYS450 4.6 22.4 1.0 C F:ILE452 4.6 19.8 1.0 CA F:HIS433 4.6 22.3 1.0 CB F:ALA455 4.7 22.4 1.0 C F:CYS431 4.7 24.7 1.0 O F:HOH2016 4.8 21.3 1.0 C F:CYS453 4.8 19.9 1.0 O F:CYS431 4.8 22.6 1.0 O F:HOH2027 4.9 36.8 1.0 CA F:ILE452 4.9 15.8 1.0 N F:ILE452 4.9 18.9 1.0 N F:ARG454 4.9 16.4 1.0 CG2 F:ILE452 4.9 21.2 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