Zinc in PDB 5vzv: TRIM23 Ring Domain

All present enzymatic activity of TRIM23 Ring Domain:
2.3.2.27;

The structure of TRIM23 Ring Domain, PDB code: 5vzv was solved by O.Pornillos, D.Dawidziak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.56 / 1.81
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.717, 142.464, 45.427, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.1

The binding sites of Zinc atom in the TRIM23 Ring Domain (pdb code 5vzv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the TRIM23 Ring Domain, PDB code: 5vzv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the TRIM23 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TRIM23 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.9 occ:1.00 SG A:CYS59 2.2 20.3 1.0 SG A:CYS56 2.3 18.3 1.0 SG A:CYS34 2.4 19.6 1.0 SG A:CYS31 2.4 15.6 1.0 HB3 A:CYS31 2.9 20.1 1.0 HB2 A:CYS59 2.9 24.4 1.0 H A:CYS34 2.9 26.4 1.0 HB3 A:CYS34 3.1 25.7 1.0 CB A:CYS31 3.1 16.6 1.0 CB A:CYS59 3.2 20.1 1.0 HB3 A:CYS56 3.2 17.4 1.0 HZ2 A:LYS44 3.3 40.9 1.0 CB A:CYS34 3.3 21.3 1.0 HB2 A:CYS31 3.3 20.1 1.0 CB A:CYS56 3.4 14.4 1.0 H A:CYS56 3.4 15.8 1.0 HB A:VAL33 3.5 23.1 1.0 HZ3 A:LYS44 3.6 40.9 1.0 H A:CYS59 3.6 23.2 1.0 N A:CYS34 3.7 21.9 1.0 HB3 A:CYS59 3.8 24.4 1.0 NZ A:LYS44 3.8 33.9 1.0 N A:CYS56 4.1 13.0 1.0 HB2 A:CYS34 4.1 25.7 1.0 CA A:CYS34 4.1 23.7 1.0 HB2 A:CYS56 4.1 17.4 1.0 HG13 A:VAL55 4.2 13.3 1.0 N A:CYS59 4.2 19.2 1.0 HZ1 A:LYS44 4.3 40.9 1.0 H A:VAL33 4.3 20.7 1.0 CA A:CYS56 4.3 11.7 1.0 CA A:CYS59 4.3 17.2 1.0 CB A:VAL33 4.5 19.1 1.0 HG12 A:VAL55 4.5 13.3 1.0 HD3 A:LYS44 4.5 39.3 1.0 CA A:CYS31 4.6 15.3 1.0 HA A:CYS59 4.6 20.8 1.0 O A:CYS56 4.7 11.8 1.0 H A:ASP36 4.7 30.3 1.0 H A:GLU35 4.8 25.5 1.0 HB2 A:ASP36 4.8 34.1 1.0 C A:VAL33 4.8 20.6 1.0 CG1 A:VAL55 4.8 11.0 1.0 C A:CYS56 4.8 10.8 1.0 HD2 A:LYS44 4.8 39.3 1.0 HG12 A:VAL33 4.8 26.8 1.0 HA A:CYS34 4.9 28.6 1.0 HB3 A:ASP58 4.9 29.8 1.0 N A:VAL33 4.9 17.1 1.0 C A:CYS31 5.0 18.9 1.0 CA A:VAL33 5.0 18.6 1.0 C A:CYS34 5.0 24.0 1.0

Zinc binding site 2 out of 6 in the TRIM23 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TRIM23 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:10.9 occ:1.00 ND1 A:HIS53 2.0 12.5 1.0 OD2 A:ASP75 2.1 17.8 1.0 SG A:CYS72 2.1 10.7 1.0 SG A:CYS51 2.3 10.6 1.0 CG A:ASP75 2.8 17.8 1.0 HB2 A:HIS53 2.8 8.1 1.0 CE1 A:HIS53 3.0 12.4 1.0 OD1 A:ASP75 3.0 13.8 1.0 HB2 A:CYS51 3.0 15.2 1.0 CG A:HIS53 3.1 12.0 1.0 HB2 A:CYS72 3.1 12.5 1.0 HE1 A:HIS53 3.1 15.1 1.0 CB A:CYS72 3.2 10.2 1.0 CB A:CYS51 3.2 12.5 1.0 HB3 A:CYS72 3.3 12.5 1.0 CB A:HIS53 3.5 6.6 1.0 HB3 A:CYS51 3.6 15.2 1.0 HB2 A:PHE74 3.7 20.5 1.0 HD2 A:PHE74 3.8 15.7 1.0 H A:HIS53 3.8 10.3 1.0 H A:ASP75 3.8 21.2 1.0 HB3 A:HIS53 4.0 8.1 1.0 NE2 A:HIS53 4.1 15.0 1.0 CB A:ASP75 4.2 15.5 1.0 CD2 A:HIS53 4.2 15.7 1.0 HD12 A:LEU49 4.3 17.4 1.0 HB2 A:GLN77 4.3 24.9 1.0 HB3 A:ASP75 4.3 18.8 1.0 O A:HOH319 4.3 30.7 1.0 H A:PHE74 4.4 20.2 1.0 N A:ASP75 4.4 17.5 1.0 N A:HIS53 4.5 8.4 1.0 CA A:CYS51 4.5 14.5 1.0 HB2 A:LEU49 4.6 10.8 1.0 CA A:HIS53 4.6 7.3 1.0 CA A:CYS72 4.6 12.1 1.0 CD2 A:PHE74 4.6 12.9 1.0 CB A:PHE74 4.7 16.9 1.0 C A:CYS51 4.7 12.5 1.0 H A:GLN77 4.7 21.9 1.0 HD13 A:LEU49 4.8 17.4 1.0 H A:CYS51 4.8 11.1 1.0 HB2 A:ASP75 4.8 18.8 1.0 HA A:CYS72 4.9 14.7 1.0 O A:CYS51 4.9 12.1 1.0 CA A:ASP75 4.9 17.3 1.0 O A:HOH309 4.9 12.1 1.0 HE2 A:HIS53 4.9 18.2 1.0 CD1 A:LEU49 5.0 14.3 1.0

Zinc binding site 3 out of 6 in the TRIM23 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of TRIM23 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:23.7 occ:1.00 SG B:CYS59 2.2 20.3 1.0 SG B:CYS56 2.3 19.8 1.0 SG B:CYS34 2.3 30.3 1.0 SG B:CYS31 2.5 19.0 1.0 HB3 B:CYS31 2.9 21.9 1.0 H B:CYS34 2.9 39.7 1.0 HB2 B:CYS59 3.0 27.9 1.0 HB3 B:CYS56 3.1 22.2 1.0 CB B:CYS31 3.1 18.1 1.0 HB3 B:CYS34 3.1 37.7 1.0 CB B:CYS59 3.2 23.1 1.0 HZ2 B:LYS44 3.3 42.3 1.0 CB B:CYS56 3.3 18.4 1.0 CB B:CYS34 3.3 31.3 1.0 HB2 B:CYS31 3.3 21.9 1.0 H B:CYS56 3.4 15.3 1.0 HZ3 B:LYS44 3.4 42.3 1.0 HB B:VAL33 3.4 34.4 1.0 H B:CYS59 3.6 25.1 1.0 N B:CYS34 3.7 33.0 1.0 NZ B:LYS44 3.8 35.1 1.0 O B:HOH303 3.8 32.6 1.0 HB3 B:CYS59 3.8 27.9 1.0 HB2 B:CYS56 4.1 22.2 1.0 N B:CYS56 4.1 12.6 1.0 HB2 B:CYS34 4.1 37.7 1.0 CA B:CYS34 4.1 40.2 1.0 HZ1 B:LYS44 4.1 42.3 1.0 HG13 B:VAL55 4.2 25.2 1.0 H B:VAL33 4.2 30.4 1.0 CA B:CYS56 4.2 12.9 1.0 N B:CYS59 4.3 20.8 1.0 CA B:CYS59 4.4 19.6 1.0 CB B:VAL33 4.4 28.5 1.0 HG12 B:VAL55 4.5 25.2 1.0 HD3 B:LYS44 4.5 45.8 1.0 CA B:CYS31 4.6 25.0 1.0 HA B:CYS59 4.7 23.8 1.0 H B:ASP36 4.7 37.6 1.0 HB2 B:ASP36 4.7 42.0 1.0 C B:VAL33 4.7 31.8 1.0 O B:CYS56 4.8 10.7 1.0 H B:GLU35 4.8 41.0 1.0 CG1 B:VAL55 4.8 20.9 1.0 C B:CYS56 4.8 11.6 1.0 HG12 B:VAL33 4.8 31.1 1.0 HA B:CYS34 4.9 48.4 1.0 HD2 B:LYS44 4.9 45.8 1.0 N B:VAL33 4.9 25.2 1.0 CA B:VAL33 4.9 31.3 1.0 HB3 B:ASP58 4.9 21.6 1.0 C B:CYS31 5.0 28.2 1.0 CE B:LYS44 5.0 40.5 1.0 CD B:LYS44 5.0 38.0 1.0

Zinc binding site 4 out of 6 in the TRIM23 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of TRIM23 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:14.8 occ:1.00 ND1 B:HIS53 2.0 10.9 1.0 OD2 B:ASP75 2.0 18.4 1.0 SG B:CYS51 2.3 14.6 1.0 SG B:CYS72 2.3 18.0 1.0 CG B:ASP75 2.8 21.3 1.0 HB2 B:HIS53 2.9 17.8 1.0 CE1 B:HIS53 2.9 15.4 1.0 OD1 B:ASP75 3.0 20.0 1.0 HE1 B:HIS53 3.0 18.7 1.0 CG B:HIS53 3.0 14.6 1.0 HB2 B:CYS51 3.1 22.7 1.0 HB2 B:CYS72 3.1 24.6 1.0 CB B:CYS72 3.2 20.4 1.0 HB3 B:CYS72 3.3 24.6 1.0 CB B:CYS51 3.3 18.8 1.0 CB B:HIS53 3.5 14.7 1.0 HB2 B:PHE74 3.6 24.4 1.0 HB3 B:CYS51 3.7 22.7 1.0 HD2 B:PHE74 3.8 27.8 1.0 H B:HIS53 3.8 12.6 1.0 H B:ASP75 3.9 22.5 1.0 HB3 B:HIS53 4.0 17.8 1.0 NE2 B:HIS53 4.0 10.3 1.0 CD2 B:HIS53 4.1 14.5 1.0 CB B:ASP75 4.1 22.2 1.0 HB2 B:GLN77 4.2 28.7 1.0 HD12 B:LEU49 4.3 22.0 1.0 HB3 B:ASP75 4.3 26.9 1.0 H B:PHE74 4.4 24.2 1.0 N B:ASP75 4.4 18.6 1.0 N B:HIS53 4.4 10.3 1.0 CA B:CYS51 4.6 14.4 1.0 CA B:HIS53 4.6 10.1 1.0 CB B:PHE74 4.6 20.2 1.0 O B:HOH326 4.6 27.5 1.0 HB2 B:LEU49 4.6 15.6 1.0 CD2 B:PHE74 4.6 23.0 1.0 CA B:CYS72 4.6 23.4 1.0 HD13 B:LEU49 4.7 22.0 1.0 C B:CYS51 4.7 15.3 1.0 O B:HOH315 4.7 23.2 1.0 H B:GLN77 4.8 30.3 1.0 O B:CYS51 4.8 15.5 1.0 H B:CYS51 4.8 19.3 1.0 HB2 B:ASP75 4.8 26.9 1.0 HE2 B:HIS53 4.8 12.5 1.0 CA B:ASP75 4.9 25.4 1.0 HA B:CYS72 4.9 28.2 1.0 CD1 B:LEU49 4.9 18.2 1.0 HD2 B:HIS53 5.0 17.6 1.0

Zinc binding site 5 out of 6 in the TRIM23 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of TRIM23 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:17.8 occ:1.00 SG C:CYS59 2.3 19.3 1.0 SG C:CYS31 2.3 14.9 1.0 SG C:CYS56 2.3 16.8 1.0 SG C:CYS34 2.4 21.9 1.0 HB3 C:CYS31 2.9 19.0 1.0 H C:CYS34 2.9 22.3 1.0 HB2 C:CYS59 3.0 18.5 1.0 HB3 C:CYS34 3.1 26.3 1.0 CB C:CYS31 3.1 15.7 1.0 HB3 C:CYS56 3.2 15.4 1.0 CB C:CYS59 3.2 15.2 1.0 HB2 C:CYS31 3.3 19.0 1.0 HZ2 C:LYS44 3.3 42.9 1.0 CB C:CYS34 3.3 21.7 1.0 CB C:CYS56 3.4 12.7 1.0 HZ3 C:LYS44 3.4 42.9 1.0 H C:CYS56 3.4 16.1 1.0 HB C:VAL33 3.5 28.1 1.0 H C:CYS59 3.6 18.9 1.0 N C:CYS34 3.6 18.4 1.0 NZ C:LYS44 3.8 35.6 1.0 HB3 C:CYS59 3.8 18.5 1.0 O C:HOH305 4.1 24.9 1.0 CA C:CYS34 4.1 24.1 1.0 HB2 C:CYS34 4.1 26.3 1.0 N C:CYS56 4.1 13.3 1.0 HB2 C:CYS56 4.1 15.4 1.0 HZ1 C:LYS44 4.2 42.9 1.0 H C:VAL33 4.2 26.4 1.0 HG13 C:VAL55 4.2 19.6 1.0 CA C:CYS56 4.3 11.6 1.0 N C:CYS59 4.3 15.5 1.0 CA C:CYS59 4.3 14.8 1.0 HD3 C:LYS44 4.4 39.1 1.0 CB C:VAL33 4.4 23.2 1.0 HG12 C:VAL55 4.5 19.6 1.0 CA C:CYS31 4.5 16.1 1.0 HA C:CYS59 4.7 18.0 1.0 C C:VAL33 4.7 25.6 1.0 H C:ASP36 4.7 25.8 1.0 H C:GLU35 4.7 26.2 1.0 O C:CYS56 4.7 11.6 1.0 HD2 C:LYS44 4.8 39.1 1.0 HB2 C:ASP36 4.8 36.3 1.0 HA C:CYS34 4.8 29.1 1.0 C C:CYS56 4.8 10.9 1.0 CG1 C:VAL55 4.8 16.2 1.0 HB3 C:ASP58 4.9 28.7 1.0 N C:VAL33 4.9 21.8 1.0 HG12 C:VAL33 4.9 28.8 1.0 CA C:VAL33 4.9 17.1 1.0 C C:CYS31 4.9 17.4 1.0 CD C:LYS44 4.9 32.4 1.0 C C:CYS34 5.0 23.2 1.0 CE C:LYS44 5.0 33.5 1.0 HA C:CYS31 5.0 19.6 1.0

Zinc binding site 6 out of 6 in the TRIM23 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of TRIM23 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:12.4 occ:1.00 ND1 C:HIS53 2.0 12.7 1.0 OD2 C:ASP75 2.0 18.4 1.0 SG C:CYS72 2.2 13.2 1.0 SG C:CYS51 2.3 10.9 1.0 CG C:ASP75 2.8 18.4 1.0 HB2 C:HIS53 2.9 15.2 1.0 CE1 C:HIS53 2.9 16.7 1.0 HB2 C:CYS72 3.0 15.9 1.0 OD1 C:ASP75 3.0 16.3 1.0 CB C:CYS72 3.0 13.1 1.0 HE1 C:HIS53 3.1 20.3 1.0 CG C:HIS53 3.1 15.9 1.0 HB2 C:CYS51 3.1 14.2 1.0 HB3 C:CYS72 3.2 15.9 1.0 CB C:CYS51 3.3 11.7 1.0 CB C:HIS53 3.5 12.5 1.0 HB3 C:CYS51 3.7 14.2 1.0 H C:HIS53 3.8 13.6 1.0 HB2 C:PHE74 3.8 25.6 1.0 H C:ASP75 3.8 20.5 1.0 HD2 C:PHE74 3.9 21.7 1.0 HB3 C:HIS53 4.1 15.2 1.0 NE2 C:HIS53 4.1 14.7 1.0 CB C:ASP75 4.1 19.0 1.0 CD2 C:HIS53 4.1 16.5 1.0 HB3 C:ASP75 4.2 23.0 1.0 HB2 C:GLN77 4.3 24.1 1.0 O C:HOH321 4.4 25.3 1.0 N C:ASP75 4.4 16.9 1.0 H C:PHE74 4.4 14.8 1.0 N C:HIS53 4.4 11.2 1.0 HD12 C:LEU49 4.4 16.4 1.0 CA C:CYS72 4.5 12.4 1.0 CA C:HIS53 4.6 9.9 1.0 HB2 C:LEU49 4.6 14.5 1.0 CA C:CYS51 4.6 13.2 1.0 HA C:CYS72 4.7 15.1 1.0 CD2 C:PHE74 4.7 17.9 1.0 CB C:PHE74 4.7 21.2 1.0 O C:HOH322 4.7 14.1 1.0 H C:GLN77 4.8 18.4 1.0 C C:CYS51 4.8 16.2 1.0 HB2 C:ASP75 4.8 23.0 1.0 HE2 C:HIS53 4.8 17.9 1.0 CA C:ASP75 4.8 14.3 1.0 HD13 C:LEU49 4.8 16.4 1.0 H C:CYS51 4.8 16.9 1.0 O C:CYS51 4.9 12.2 1.0

D.M.Dawidziak, J.G.Sanchez, J.M.Wagner, B.K.Ganser-Pornillos, O.Pornillos. Structure and Catalytic Activation of the TRIM23 Ring E3 Ubiquitin Ligase. Proteins V. 85 1957 2017.
ISSN: ESSN 1097-0134
PubMed: 28681414
DOI: 10.1002/PROT.25348