Zinc in PDB 7m4o: Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin

All present enzymatic activity of Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin:
2.3.2.27;

The structure of Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin, PDB code: 7m4o was solved by T.R.Cotton, B.C.Lechtenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.05 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.526, 84.216, 90.095, 90, 90, 90
R / Rfree (%)	20.1 / 25.2

The binding sites of Zinc atom in the Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin (pdb code 7m4o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin, PDB code: 7m4o:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:36.0 occ:1.00 SG A:CYS695 2.2 35.1 1.0 SG A:CYS675 2.3 33.3 1.0 SG A:CYS693 2.3 38.0 1.0 SG A:CYS678 2.3 34.5 1.0 CB A:CYS695 3.0 40.0 1.0 CB A:CYS675 3.1 37.0 1.0 CB A:CYS693 3.2 36.3 1.0 CB A:CYS678 3.4 37.8 1.0 N A:CYS678 3.8 35.4 1.0 N A:CYS695 4.0 40.3 1.0 CA A:CYS695 4.1 38.1 1.0 CA A:CYS678 4.1 39.4 1.0 CB A:LYS677 4.4 39.8 1.0 CA A:CYS675 4.6 37.9 1.0 CA A:CYS693 4.6 37.2 1.0 CB A:ALA697 4.8 34.4 1.0 C A:CYS678 4.8 35.6 1.0 C A:LYS677 4.8 39.1 1.0 C A:CYS695 4.9 40.9 1.0 OG1 A:THR680 4.9 45.3 1.0 C A:CYS693 4.9 39.0 1.0 CB A:THR680 4.9 37.8 1.0 N A:GLY679 4.9 36.1 1.0 N A:ARG694 4.9 41.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:31.2 occ:1.00 NE2 A:HIS712 2.1 34.0 1.0 SG A:CYS700 2.2 30.3 1.0 SG A:CYS730 2.3 31.3 1.0 SG A:CYS703 2.4 30.7 1.0 CE1 A:HIS712 2.8 36.2 1.0 CB A:CYS700 3.0 31.6 1.0 CB A:CYS730 3.1 33.1 1.0 CD2 A:HIS712 3.2 31.4 1.0 CB A:CYS703 3.4 39.5 1.0 N A:CYS703 3.7 35.0 1.0 ND1 A:HIS712 4.0 33.2 1.0 CA A:CYS703 4.1 37.2 1.0 CG A:HIS712 4.3 32.7 1.0 CA A:CYS700 4.5 34.9 1.0 CB A:LEU702 4.6 37.8 1.0 CA A:CYS730 4.6 39.8 1.0 CE2 A:PHE713 4.8 32.5 1.0 C A:LEU702 4.8 38.1 1.0 C A:CYS703 4.9 37.5 1.0 CG1 A:VAL705 4.9 37.7 1.0 C A:CYS700 4.9 30.2 1.0 N A:LEU702 5.0 30.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Phosphorylated Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:35.8 occ:1.00 ND1 A:HIS716 2.0 33.8 1.0 SG A:CYS724 2.2 33.4 1.0 SG A:CYS727 2.4 34.4 1.0 SG A:CYS714 2.4 33.2 1.0 CE1 A:HIS716 2.9 43.7 1.0 CG A:HIS716 3.0 41.8 1.0 CB A:CYS714 3.2 32.1 1.0 CB A:CYS724 3.2 39.2 1.0 CB A:HIS716 3.4 33.0 1.0 CB A:CYS727 3.5 37.7 1.0 N A:CYS727 3.7 43.2 1.0 CA A:CYS714 3.9 31.6 1.0 CA A:CYS727 4.0 34.0 1.0 NE2 A:HIS716 4.0 51.7 1.0 CD2 A:HIS716 4.1 45.7 1.0 O A:HOH908 4.1 28.7 1.0 O A:CYS727 4.2 41.9 1.0 N A:HIS716 4.2 36.4 1.0 C A:CYS727 4.3 41.4 1.0 CA A:HIS716 4.5 35.6 1.0 CB A:GLU726 4.5 43.8 1.0 C A:GLU726 4.5 47.5 1.0 C A:CYS714 4.5 35.2 1.0 N A:GLN715 4.5 34.6 1.0 CA A:CYS724 4.7 39.9 1.0 N A:GLU726 4.8 44.4 1.0 CA A:GLU726 4.8 40.8 1.0 NH2 A:ARG718 4.8 41.5 1.0 O A:HOH921 4.8 44.4 1.0

T.R.Cotton, S.A.Cobbold, J.P.Bernardini, L.W.Richardson, X.S.Wang, B.C.Lechtenberg. Structural Basis of K63-Ubiquitin Chain Formation By the Gordon-Holmes Syndrome Rbr E3 Ubiquitin Ligase RNF216 Mol.Cell 2022.
ISSN: ISSN 1097-2765