Zinc in PDB 7xz1: Trim E3 Ubiquitin Ligase

The structure of Trim E3 Ubiquitin Ligase, PDB code: 7xz1 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)	38.86 / 5.20
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	235.921, 235.921, 158.814, 90, 90, 90
R / Rfree (%)	26.6 / 31.5

The binding sites of Zinc atom in the Trim E3 Ubiquitin Ligase (pdb code 7xz1). 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: 7xz1:
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:541.0 occ:1.00 ND1 A:HIS89 1.9 417.1 1.0 SG A:CYS86 2.1 432.1 1.0 SG A:CYS108 2.2 508.5 1.0 SG A:CYS105 2.4 333.4 1.0 CE1 A:HIS89 2.7 420.8 1.0 CG A:HIS89 3.0 445.8 1.0 CB A:HIS89 3.5 386.9 1.0 CB A:CYS108 3.5 384.6 1.0 N A:CYS108 3.5 450.8 1.0 CB A:CYS86 3.7 354.0 1.0 NE2 A:HIS89 3.8 430.7 1.0 CD2 A:HIS89 3.9 468.7 1.0 CA A:CYS108 4.0 385.9 1.0 OD1 A:ASP91 4.1 397.3 1.0 CB A:CYS105 4.2 331.2 1.0 CB A:VAL107 4.3 316.4 1.0 C A:VAL107 4.4 423.6 1.0 CA A:VAL107 4.7 315.0 1.0 N A:VAL107 4.7 314.8 1.0 CA A:HIS89 4.8 455.3 1.0 N A:HIS89 4.8 496.5 1.0 CA A:CYS86 4.9 409.6 1.0 CG2 A:VAL107 4.9 312.5 1.0 CG A:ASP91 5.0 426.2 1.0 OD2 A:ASP91 5.0 319.8 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:443.8 occ:1.00 CE1 A:HIS114 1.7 436.2 1.0 ND1 A:HIS117 2.0 522.0 1.0 ND1 A:HIS114 2.0 424.8 1.0 OD2 A:ASP100 2.1 564.9 1.0 SG A:CYS97 2.3 415.1 1.0 NE2 A:HIS114 2.3 359.9 1.0 CG A:HIS117 2.6 355.9 1.0 CG A:ASP100 2.7 508.1 1.0 CG A:HIS114 2.7 349.0 1.0 CE1 A:HIS117 2.8 606.3 1.0 CD2 A:HIS114 2.9 351.1 1.0 CB A:HIS117 3.1 350.2 1.0 CB A:ASP100 3.3 430.3 1.0 CD2 A:HIS117 3.5 356.1 1.0 NE2 A:HIS117 3.5 592.4 1.0 OD1 A:ASP100 3.6 510.5 1.0 CB A:CYS97 3.9 462.2 1.0 CB A:HIS114 3.9 340.9 1.0 N A:ASP100 4.1 518.7 1.0 O A:SER113 4.2 665.6 1.0 CA A:ASP100 4.3 441.3 1.0 CA A:HIS114 4.4 341.6 1.0 CA A:HIS117 4.6 361.8 1.0 C A:GLN99 4.7 547.6 1.0 CB A:GLN99 4.7 478.3 1.0 C A:SER113 5.0 542.8 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:357.9 occ:1.00 ND1 B:HIS89 2.0 571.8 1.0 SG B:CYS105 2.2 360.4 1.0 SG B:CYS86 2.2 326.1 1.0 SG B:CYS108 2.3 584.1 1.0 CE1 B:HIS89 2.4 598.1 1.0 CG B:HIS89 3.2 600.6 1.0 NE2 B:HIS89 3.5 649.4 1.0 CB B:CYS108 3.7 501.2 1.0 N B:CYS108 3.8 421.6 1.0 CB B:CYS86 3.8 395.4 1.0 CB B:CYS105 3.8 382.1 1.0 CD2 B:HIS89 3.9 624.4 1.0 CB B:HIS89 3.9 537.6 1.0 CD2 B:LEU93 4.3 463.4 1.0 CB B:VAL107 4.3 556.0 1.0 CA B:CYS108 4.3 421.3 1.0 N B:CYS105 4.7 445.1 1.0 C B:VAL107 4.7 432.0 1.0 CA B:CYS105 4.7 416.0 1.0 N B:VAL107 4.9 431.1 1.0 CA B:VAL107 4.9 440.1 1.0 N B:HIS89 5.0 587.8 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:452.1 occ:1.00 CE1 B:HIS114 1.6 424.2 1.0 ND1 B:HIS117 2.0 407.5 1.0 OD2 B:ASP100 2.1 375.9 1.0 ND1 B:HIS114 2.1 467.1 1.0 NE2 B:HIS114 2.3 383.6 1.0 CG B:HIS117 2.4 508.7 1.0 SG B:CYS97 2.4 495.8 1.0 CE1 B:HIS117 2.6 380.2 1.0 CG B:ASP100 2.7 407.8 1.0 CG B:HIS114 2.9 458.8 1.0 CB B:HIS117 3.0 510.3 1.0 CD2 B:HIS114 3.0 439.6 1.0 CB B:ASP100 3.1 407.3 1.0 CD2 B:HIS117 3.1 468.2 1.0 NE2 B:HIS117 3.2 384.3 1.0 OD1 B:ASP100 3.7 549.5 1.0 CB B:CYS97 3.9 504.3 1.0 O B:SER113 4.1 396.6 1.0 CB B:HIS114 4.2 442.0 1.0 CA B:ASP100 4.3 499.4 1.0 N B:ASP100 4.3 397.8 1.0 CA B:HIS117 4.5 393.4 1.0 CG B:GLN99 4.5 366.1 1.0 CA B:HIS114 4.7 386.7 1.0

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