Zinc in PDB 8gcb: Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate

All present enzymatic activity of Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The structure of Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate, PDB code: 8gcb was solved by A.J.Middleton, C.L.Day, T.J.Fokkens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.50 / 2.39
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.325, 59.325, 185.821, 90, 90, 90
R / Rfree (%)	25.3 / 27.1

The binding sites of Zinc atom in the Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate (pdb code 8gcb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate, PDB code: 8gcb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:62.7 occ:1.00 SG B:CYS40 2.3 61.0 1.0 SG B:CYS60 2.3 62.0 1.0 SG B:CYS57 2.3 61.5 1.0 SG B:CYS37 2.3 61.1 1.0 CB B:CYS37 3.1 57.5 1.0 CB B:CYS57 3.2 58.7 1.0 CB B:CYS60 3.3 61.2 1.0 CB B:CYS40 3.3 58.5 1.0 N B:CYS40 3.8 53.8 1.0 N B:CYS57 3.9 57.1 1.0 CA B:CYS40 4.2 57.9 1.0 CA B:CYS57 4.2 58.2 1.0 CA B:CYS37 4.5 55.5 1.0 NH2 B:ARG113 4.6 71.2 1.0 CA B:CYS60 4.6 60.1 1.0 CB B:VAL39 4.7 53.4 1.0 C B:VAL39 4.9 53.0 1.0 N B:CYS60 5.0 60.5 1.0 C B:CYS37 5.0 56.4 1.0 C B:CYS40 5.0 59.6 1.0

Zinc binding site 2 out of 3 in the Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:62.3 occ:1.00 ND1 B:HIS54 2.0 53.7 1.0 SG B:CYS52 2.3 65.7 1.0 SG B:CYS72 2.3 60.1 1.0 SG B:CYS75 2.4 66.1 1.0 CE1 B:HIS54 2.9 57.5 1.0 CG B:HIS54 3.0 58.6 1.0 CB B:CYS52 3.2 66.0 1.0 CB B:CYS72 3.3 59.4 1.0 CB B:CYS75 3.4 72.0 1.0 CB B:HIS54 3.5 57.3 1.0 N B:CYS75 3.9 74.3 1.0 NE2 B:HIS54 4.0 55.9 1.0 CD2 B:HIS54 4.1 54.5 1.0 OG1 B:THR50 4.1 68.2 1.0 CA B:CYS75 4.2 76.0 1.0 CA B:CYS52 4.4 61.9 1.0 O B:CYS52 4.5 63.8 1.0 C B:CYS52 4.6 61.6 1.0 CB B:TYR74 4.6 65.4 1.0 CA B:CYS72 4.7 63.1 1.0 N B:HIS54 4.7 56.4 1.0 CD2 B:TYR74 4.7 65.1 1.0 CA B:HIS54 4.7 57.7 1.0 C B:CYS75 4.9 76.7 1.0 CB B:ALA77 4.9 71.5 1.0 C B:TYR74 5.0 72.0 1.0

Zinc binding site 3 out of 3 in the Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of RNF125 in Complex with A UBCH5B~Ub Conjugate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:65.2 occ:1.00 NE2 B:HIS115 1.9 60.0 1.0 SG B:CYS119 2.3 60.2 1.0 SG B:CYS103 2.3 66.5 1.0 SG B:CYS100 2.3 67.8 1.0 CE1 B:HIS115 2.9 58.2 1.0 CD2 B:HIS115 2.9 58.8 1.0 CB B:CYS100 3.2 69.2 1.0 CB B:CYS103 3.3 69.6 1.0 CB B:CYS119 3.3 60.6 1.0 N B:CYS103 3.9 70.7 1.0 ND1 B:HIS115 4.0 57.0 1.0 CG B:HIS115 4.0 56.6 1.0 CA B:CYS103 4.1 67.6 1.0 CG2 B:THR105 4.2 80.2 1.0 CA B:CYS119 4.4 58.3 1.0 CA B:CYS100 4.6 71.3 1.0 C B:CYS103 4.8 69.2 1.0 N B:ASP104 4.8 69.2 1.0 CD1 B:TYR122 4.8 90.4 1.0 CB B:GLU102 4.9 80.3 1.0 C B:GLU102 4.9 75.2 1.0

A.J.Middleton, F.Barzak, T.Fokkens, K.Nguyen, C.L.Day. Zinc Finger 1 of the Ring E3 Ligase, RNF125, Interacts with the E2 to Enhance Ubiquitylation Structure 2023.
ISSN: ISSN 0969-2126