Zinc in PDB 5fer: Complex of TRIM25 Ring with UBCH5-Ub

All present enzymatic activity of Complex of TRIM25 Ring with UBCH5-Ub:
2.3.2.23; 2.3.2.24; 2.3.2.27;

The structure of Complex of TRIM25 Ring with UBCH5-Ub, PDB code: 5fer was solved by K.Rittinger, M.G.Koliopoulos, D.Esposito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.30 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.480, 71.700, 160.430, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27.3

The binding sites of Zinc atom in the Complex of TRIM25 Ring with UBCH5-Ub (pdb code 5fer). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Complex of TRIM25 Ring with UBCH5-Ub, PDB code: 5fer:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Complex of TRIM25 Ring with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of TRIM25 Ring with UBCH5-Ub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:71.5 occ:0.93 SG A:CYS16 2.3 47.6 1.0 SG A:CYS33 2.3 46.3 1.0 SG A:CYS36 2.4 54.8 1.0 SG A:CYS13 2.5 41.6 1.0 CB A:CYS33 2.8 30.8 1.0 CB A:CYS13 3.1 29.3 1.0 CB A:CYS36 3.3 31.5 1.0 CB A:CYS16 3.4 34.2 1.0 NZ A:LYS21 3.6 49.9 1.0 N A:CYS16 3.7 45.8 1.0 N A:CYS33 3.7 29.7 1.0 CA A:CYS33 3.9 35.4 1.0 CA A:CYS16 4.2 43.0 1.0 CB A:ILE15 4.5 42.2 1.0 CA A:CYS13 4.6 39.8 1.0 CA A:CYS36 4.6 37.8 1.0 CE A:LYS21 4.8 55.5 1.0 C A:ILE15 4.8 43.7 1.0 N A:CYS36 4.8 42.1 1.0 C A:CYS33 4.9 33.4 1.0 N A:ILE15 4.9 34.4 1.0 CG2 A:ILE15 5.0 37.7 1.0 C A:PHE32 5.0 34.5 1.0 CA A:ILE15 5.0 43.8 1.0

Zinc binding site 2 out of 4 in the Complex of TRIM25 Ring with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of TRIM25 Ring with UBCH5-Ub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:38.3 occ:0.67 ND1 A:HIS30 2.1 39.1 1.0 SG A:CYS28 2.3 38.5 1.0 SG A:CYS53 2.3 36.0 1.0 SG A:CYS50 2.4 32.0 1.0 CE1 A:HIS30 2.8 38.2 1.0 CB A:CYS50 3.2 40.7 1.0 CG A:HIS30 3.2 45.7 1.0 CB A:CYS28 3.2 35.7 1.0 CB A:CYS53 3.7 32.9 1.0 CB A:HIS30 3.7 32.2 1.0 OG1 A:THR26 4.0 34.3 1.0 N A:CYS53 4.0 39.1 1.0 NE2 A:HIS30 4.0 42.8 1.0 CD2 A:HIS30 4.2 35.0 1.0 O A:CYS28 4.3 37.6 1.0 CA A:CYS28 4.4 34.1 1.0 C A:CYS28 4.4 40.4 1.0 CA A:CYS53 4.4 39.6 1.0 CB A:ALA55 4.6 39.7 1.0 N A:HIS30 4.6 34.3 1.0 CA A:CYS50 4.6 37.8 1.0 CB A:GLN52 4.7 31.4 1.0 CA A:HIS30 4.8 41.5 1.0 C A:GLN52 4.8 35.4 1.0 N A:GLN52 5.0 33.3 1.0 C A:CYS53 5.0 45.1 1.0

Zinc binding site 3 out of 4 in the Complex of TRIM25 Ring with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex of TRIM25 Ring with UBCH5-Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:41.5 occ:0.69 ND1 D:HIS30 2.1 35.0 1.0 SG D:CYS53 2.3 40.6 1.0 SG D:CYS28 2.3 44.6 1.0 SG D:CYS50 2.4 37.6 1.0 CE1 D:HIS30 2.8 44.3 1.0 CB D:CYS50 3.2 41.8 1.0 CG D:HIS30 3.2 44.1 1.0 CB D:CYS28 3.3 40.7 1.0 CB D:CYS53 3.5 38.6 1.0 CB D:HIS30 3.7 35.6 1.0 N D:CYS53 3.9 41.3 1.0 NE2 D:HIS30 4.0 45.2 1.0 OG1 D:THR26 4.0 35.3 1.0 CD2 D:HIS30 4.2 46.3 1.0 CA D:CYS53 4.3 46.3 1.0 O D:CYS28 4.3 41.1 1.0 CA D:CYS28 4.4 41.5 1.0 C D:CYS28 4.5 40.3 1.0 CB D:ALA55 4.5 37.6 1.0 CA D:CYS50 4.7 40.0 1.0 N D:HIS30 4.7 35.6 1.0 C D:GLN52 4.8 38.7 1.0 C D:CYS53 4.8 48.3 1.0 CB D:GLN52 4.8 35.7 1.0 CA D:HIS30 4.9 41.3 1.0 N D:ALA55 5.0 44.1 1.0

Zinc binding site 4 out of 4 in the Complex of TRIM25 Ring with UBCH5-Ub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex of TRIM25 Ring with UBCH5-Ub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:48.7 occ:0.67 SG D:CYS33 2.3 46.6 1.0 SG D:CYS16 2.3 54.9 1.0 SG D:CYS36 2.3 43.3 1.0 SG D:CYS13 2.4 41.6 1.0 CB D:CYS13 2.9 36.8 1.0 CB D:CYS33 3.1 38.4 1.0 CB D:CYS16 3.3 45.0 1.0 CB D:CYS36 3.5 48.4 1.0 N D:CYS16 3.7 47.0 1.0 N D:CYS33 4.0 32.2 1.0 CA D:CYS16 4.1 43.7 1.0 CA D:CYS33 4.1 38.2 1.0 CE D:LYS21 4.4 66.8 1.0 CA D:CYS13 4.4 41.9 1.0 NZ D:LYS21 4.5 63.3 1.0 CB D:ILE15 4.6 42.0 1.0 CA D:CYS36 4.8 39.3 1.0 C D:ILE15 4.8 42.2 1.0 C D:CYS13 4.9 38.4 1.0 N D:ILE15 4.9 41.6 1.0 C D:CYS16 5.0 46.7 1.0

M.G.Koliopoulos, D.Esposito, E.Christodoulou, I.A.Taylor, K.Rittinger. Functional Role of Trim E3 Ligase Oligomerization and Regulation of Catalytic Activity. Embo J. V. 35 1204 2016.
ISSN: ESSN 1460-2075
PubMed: 27154206
DOI: 10.15252/EMBJ.201593741