Zinc in PDB 8gbq: Structure of RNF125 in Complex with UBCH5B

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

The structure of Structure of RNF125 in Complex with UBCH5B, PDB code: 8gbq 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)	41.87 / 1.74
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.181, 56.181, 164.347, 90, 90, 120
R / Rfree (%)	18.4 / 20.1

The binding sites of Zinc atom in the Structure of RNF125 in Complex with UBCH5B (pdb code 8gbq). 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 UBCH5B, PDB code: 8gbq:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of RNF125 in Complex with UBCH5B


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 UBCH5B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:29.5 occ:1.00 SG B:CYS60 2.3 33.0 1.0 SG B:CYS40 2.3 33.5 1.0 SG B:CYS37 2.4 28.4 1.0 SG B:CYS57 2.4 30.1 1.0 CB B:CYS37 3.0 27.2 1.0 CB B:CYS57 3.2 29.3 1.0 CB B:CYS40 3.3 33.8 1.0 CB B:CYS60 3.3 29.1 1.0 N B:CYS40 3.7 30.8 1.0 N B:CYS57 3.9 27.5 1.0 O B:HOH307 4.0 40.0 1.0 CA B:CYS40 4.1 32.9 1.0 CA B:CYS57 4.2 25.0 1.0 CA B:CYS37 4.5 29.8 1.0 NH2 B:ARG113 4.5 38.6 1.0 CA B:CYS60 4.7 30.7 1.0 CB B:VAL39 4.7 25.4 1.0 C B:VAL39 4.8 27.9 1.0 C B:CYS40 4.9 32.5 1.0 C B:CYS37 5.0 30.1 1.0

Zinc binding site 2 out of 3 in the Structure of RNF125 in Complex with UBCH5B


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 UBCH5B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:30.1 occ:1.00 ND1 B:HIS54 2.1 32.1 1.0 SG B:CYS52 2.3 32.1 1.0 SG B:CYS72 2.3 27.8 1.0 SG B:CYS75 2.3 32.7 1.0 CE1 B:HIS54 2.9 34.5 1.0 CB B:CYS72 3.1 31.3 1.0 CG B:HIS54 3.2 31.1 1.0 CB B:CYS52 3.3 30.8 1.0 CB B:CYS75 3.5 34.7 1.0 CB B:HIS54 3.7 31.1 1.0 N B:CYS75 3.9 35.1 1.0 NE2 B:HIS54 4.1 32.4 1.0 OG1 B:THR50 4.2 33.0 1.0 CA B:CYS75 4.2 33.9 1.0 CD2 B:HIS54 4.2 33.6 1.0 CA B:CYS52 4.5 34.0 1.0 O B:CYS52 4.5 33.8 1.0 C B:CYS52 4.5 32.2 1.0 CA B:CYS72 4.6 31.7 1.0 CB B:TYR74 4.7 30.4 1.0 CB B:ALA77 4.7 39.1 1.0 N B:HIS54 4.8 28.2 1.0 C B:CYS75 4.9 33.3 1.0 CA B:HIS54 4.9 28.4 1.0 CD2 B:TYR74 4.9 35.5 1.0 C B:TYR74 5.0 33.6 1.0 N B:ALA77 5.0 36.3 1.0

Zinc binding site 3 out of 3 in the Structure of RNF125 in Complex with UBCH5B


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 UBCH5B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:50.0 occ:1.00 NE2 B:HIS115 2.1 47.0 1.0 SG B:CYS103 2.3 59.6 1.0 SG B:CYS100 2.3 54.0 1.0 SG B:CYS119 2.3 57.0 1.0 CD2 B:HIS115 3.0 44.8 1.0 CE1 B:HIS115 3.1 47.4 1.0 CB B:CYS100 3.1 64.8 1.0 CB B:CYS119 3.3 53.1 1.0 CB B:CYS103 3.3 70.8 1.0 N B:CYS103 3.9 75.3 1.0 CA B:CYS103 4.1 73.1 1.0 CG B:HIS115 4.1 41.8 1.0 ND1 B:HIS115 4.2 42.2 1.0 CA B:CYS119 4.6 50.3 1.0 CA B:CYS100 4.6 68.2 1.0 C B:CYS103 4.8 76.9 1.0 C B:GLU102 4.8 77.8 1.0 CD2 B:TYR122 4.8 65.0 1.0 OG1 B:THR105 4.8 72.4 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