Zinc in PDB 7xz0: Trim E3 Ubiquitin Ligase

The structure of Trim E3 Ubiquitin Ligase, PDB code: 7xz0 was solved by S.H.Park, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.74 / 3.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	239.728, 72.967, 83.764, 90, 97.6, 90
R / Rfree (%)	25.4 / 30.8

The binding sites of Zinc atom in the Trim E3 Ubiquitin Ligase (pdb code 7xz0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Trim E3 Ubiquitin Ligase, PDB code: 7xz0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Trim E3 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:202.7 occ:1.00 ND1 A:HIS89 2.1 187.4 1.0 SG A:CYS105 2.3 207.8 1.0 SG A:CYS108 2.4 169.3 1.0 SG A:CYS86 2.6 158.3 1.0 CE1 A:HIS89 3.0 193.0 1.0 CG A:HIS89 3.1 171.9 1.0 CB A:CYS105 3.4 185.3 1.0 CB A:HIS89 3.5 164.3 1.0 CB A:CYS108 3.7 187.0 1.0 N A:CYS105 4.0 209.9 1.0 N A:CYS108 4.0 175.0 1.0 CB A:CYS86 4.0 176.9 1.0 CA A:CYS105 4.1 200.9 1.0 NE2 A:HIS89 4.1 202.6 1.0 CD2 A:HIS89 4.2 178.7 1.0 CA A:CYS108 4.5 173.7 1.0 C A:CYS105 4.5 174.7 1.0 N A:HIS89 4.6 178.6 1.0 CA A:HIS89 4.6 173.0 1.0 OD2 A:ASP91 4.8 210.3 1.0 O A:CYS105 4.8 183.9 1.0 N A:VAL107 4.9 185.6 1.0 CB A:VAL107 5.0 169.3 1.0

Zinc binding site 2 out of 4 in the Trim E3 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:184.7 occ:1.00 ND1 A:HIS114 1.9 150.3 1.0 ND1 A:HIS117 2.0 183.9 1.0 SG A:CYS97 2.4 158.1 1.0 CE1 A:HIS117 2.5 188.1 1.0 OD2 A:ASP100 2.7 165.2 1.0 CG A:HIS114 2.8 159.0 1.0 CE1 A:HIS114 2.9 171.6 1.0 CB A:ASP100 2.9 187.0 1.0 CG A:ASP100 3.2 158.9 1.0 CB A:HIS114 3.2 181.2 1.0 CG A:HIS117 3.3 195.5 1.0 CB A:CYS97 3.6 159.0 1.0 CA A:HIS114 3.8 180.4 1.0 NE2 A:HIS117 3.8 188.4 1.0 NE2 A:HIS114 3.9 148.4 1.0 CD2 A:HIS114 3.9 152.3 1.0 CB A:HIS117 4.0 193.8 1.0 CD2 A:HIS117 4.1 187.7 1.0 O A:SER113 4.3 170.2 1.0 CA A:ASP100 4.3 172.1 1.0 OD1 A:ASP100 4.4 163.3 1.0 N A:ASP100 4.5 172.9 1.0 CG A:GLN99 4.6 175.7 1.0 N A:HIS114 4.7 184.1 1.0 C A:SER113 4.8 186.1 1.0 C A:HIS114 4.9 182.9 1.0 CA A:CYS97 5.0 186.7 1.0

Zinc binding site 3 out of 4 in the Trim E3 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:220.9 occ:1.00 ND1 B:HIS89 2.2 211.9 1.0 SG B:CYS105 2.2 215.2 1.0 SG B:CYS108 2.3 204.1 1.0 SG B:CYS86 2.5 232.5 1.0 CG B:HIS89 3.0 214.2 1.0 CB B:HIS89 3.2 213.2 1.0 CE1 B:HIS89 3.2 213.7 1.0 CB B:CYS105 3.4 201.5 1.0 CB B:CYS108 3.4 211.9 1.0 N B:CYS108 3.6 223.5 1.0 N B:CYS105 3.9 196.9 1.0 CB B:CYS86 3.9 221.8 1.0 CA B:CYS105 4.1 206.5 1.0 CA B:CYS108 4.1 214.2 1.0 CD2 B:HIS89 4.2 223.8 1.0 N B:HIS89 4.3 213.9 1.0 NE2 B:HIS89 4.3 226.0 1.0 CA B:HIS89 4.3 214.8 1.0 C B:CYS105 4.4 206.5 1.0 O B:CYS105 4.6 211.0 1.0 N B:VAL107 4.7 205.7 1.0 C B:VAL107 4.7 229.2 1.0 CB B:VAL107 4.8 213.8 1.0 N B:GLY106 4.9 199.1 1.0 OD2 B:ASP91 5.0 240.5 1.0 CA B:VAL107 5.0 209.1 1.0

Zinc binding site 4 out of 4 in the Trim E3 Ubiquitin Ligase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:263.9 occ:1.00 ND1 B:HIS117 2.1 208.1 1.0 ND1 B:HIS114 2.1 200.4 1.0 CB B:ASP100 2.4 242.6 1.0 SG B:CYS97 2.4 194.1 1.0 CE1 B:HIS117 2.6 203.9 1.0 CE1 B:HIS114 2.6 199.9 1.0 OD2 B:ASP100 2.7 260.1 1.0 CG B:ASP100 2.8 239.4 1.0 CB B:CYS97 3.3 192.1 1.0 CG B:HIS114 3.4 232.6 1.0 CG B:HIS117 3.4 225.0 1.0 CA B:ASP100 3.6 212.1 1.0 N B:ASP100 3.8 217.1 1.0 NE2 B:HIS114 3.9 199.5 1.0 OD1 B:ASP100 3.9 241.1 1.0 NE2 B:HIS117 3.9 205.6 1.0 O B:SER113 4.0 207.8 1.0 CB B:HIS114 4.1 238.4 1.0 CB B:HIS117 4.1 228.2 1.0 CD2 B:HIS114 4.2 210.3 1.0 CD2 B:HIS117 4.3 207.7 1.0 CA B:HIS114 4.4 230.8 1.0 C B:GLN99 4.5 213.8 1.0 OG B:SER113 4.5 207.6 1.0 CA B:CYS97 4.8 188.7 1.0 C B:SER113 4.8 208.2 1.0 C B:ASP100 4.8 199.7 1.0 O B:GLN99 4.9 216.6 1.0 OE1 B:GLN99 4.9 199.5 1.0 CG B:GLN99 4.9 194.4 1.0 N B:HIS114 5.0 230.9 1.0

S.H.Park, H.K.Song. Trim E3 Ubiquitin Ligase To Be Published.