Zinc in PDB 7xyz: Trim E3 Ubiquitin Ligase

The structure of Trim E3 Ubiquitin Ligase, PDB code: 7xyz 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)	35.79 / 4.62
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	174.375, 174.375, 224.941, 90, 90, 120
R / Rfree (%)	31.2 / 34.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Trim E3 Ubiquitin Ligase (pdb code 7xyz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Trim E3 Ubiquitin Ligase, PDB code: 7xyz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 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:551.8 occ:1.00 CB A:CYS14 2.1 477.7 1.0 SG A:CYS14 2.1 527.7 1.0 SG A:CYS34 2.3 505.7 1.0 SG A:CYS37 2.3 498.1 1.0 SG A:CYS17 2.4 460.4 1.0 CB A:CYS17 2.5 415.3 1.0 CB A:CYS34 2.8 486.4 1.0 N A:CYS17 3.6 423.5 1.0 CA A:CYS14 3.6 438.0 1.0 CA A:CYS17 3.6 411.4 1.0 OD1 A:ASP22 3.9 612.3 1.0 CB A:CYS37 4.0 504.3 1.0 CG A:ASP22 4.1 631.1 1.0 NE2 A:GLN19 4.1 426.4 1.0 OD2 A:ASP22 4.1 659.4 1.0 CA A:CYS34 4.2 521.8 1.0 C A:CYS14 4.3 422.9 1.0 N A:CYS14 4.3 450.4 1.0 C A:LEU16 4.4 416.5 1.0 O A:CYS14 4.5 432.2 1.0 N A:CYS34 4.6 539.9 1.0 C A:CYS17 4.6 410.6 1.0 N A:LEU18 4.7 422.9 1.0 N A:LEU16 4.9 426.7 1.0 CB A:ASP22 5.0 639.0 1.0

Zinc binding site 2 out of 16 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:511.9 occ:1.00 ND1 A:HIS31 2.2 464.1 1.0 SG A:CYS56 2.3 454.0 1.0 SG A:CYS53 2.4 433.8 1.0 SG A:CYS29 2.4 412.2 1.0 CE1 A:HIS31 2.8 460.6 1.0 CB A:CYS56 2.9 479.2 1.0 CG A:HIS31 3.3 487.2 1.0 OG A:SER55 3.3 397.6 1.0 CB A:CYS53 3.4 460.5 1.0 N A:CYS56 3.6 495.7 1.0 CA A:CYS56 3.8 502.1 1.0 CB A:HIS31 3.9 494.4 1.0 NE2 A:HIS31 3.9 480.6 1.0 CB A:CYS29 4.2 418.5 1.0 CD2 A:HIS31 4.2 504.7 1.0 C A:SER55 4.3 457.0 1.0 O A:CYS29 4.4 435.5 1.0 CZ A:PHE33 4.6 458.3 1.0 CB A:SER55 4.6 400.2 1.0 CA A:SER55 4.8 442.7 1.0 C A:CYS56 4.8 517.1 1.0 C A:CYS29 4.9 441.1 1.0 N A:SER55 4.9 465.3 1.0 CA A:CYS53 4.9 472.3 1.0 N A:GLN57 4.9 474.0 1.0 O A:SER55 5.0 452.8 1.0

Zinc binding site 3 out of 16 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 A:Zn503 b:533.1 occ:1.00 CE1 A:HIS89 1.9 445.0 1.0 ND1 A:HIS89 2.1 438.5 1.0 SG A:CYS105 2.2 570.6 1.0 SG A:CYS86 2.4 572.6 1.0 SG A:CYS108 2.4 389.1 1.0 CB A:CYS108 3.0 370.8 1.0 NE2 A:HIS89 3.2 440.5 1.0 CG A:HIS89 3.4 422.9 1.0 N A:CYS108 3.5 416.1 1.0 CB A:CYS105 3.7 510.4 1.0 CA A:CYS108 3.8 383.2 1.0 CB A:CYS86 3.8 485.5 1.0 CB A:GLU88 3.9 473.7 1.0 CD2 A:HIS89 3.9 434.5 1.0 CB A:HIS89 4.4 416.9 1.0 N A:HIS89 4.5 473.6 1.0 O A:ASP91 4.5 447.9 1.0 C A:VAL107 4.6 394.6 1.0 CG A:GLU88 4.6 460.0 1.0 CB A:VAL107 4.6 350.4 1.0 CD A:GLU88 4.6 413.6 1.0 CA A:GLU88 4.7 485.1 1.0 N A:GLU88 4.7 481.9 1.0 C A:GLU88 4.8 482.5 1.0 CA A:CYS105 4.8 504.9 1.0 OE1 A:GLU88 4.8 393.3 1.0 O A:CYS105 4.9 508.1 1.0 C A:CYS105 5.0 497.0 1.0 CA A:VAL107 5.0 374.8 1.0

Zinc binding site 4 out of 16 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 A:Zn504 b:544.7 occ:1.00 ND1 A:HIS114 1.8 402.7 1.0 ND1 A:HIS117 2.1 476.8 1.0 SG A:CYS97 2.1 471.0 1.0 OD2 A:ASP100 2.2 482.8 1.0 CE1 A:HIS114 2.3 386.1 1.0 CE1 A:HIS117 2.4 479.7 1.0 CG A:HIS114 2.6 367.5 1.0 CG A:ASP100 2.8 463.5 1.0 OD1 A:ASP100 2.8 444.4 1.0 CB A:CYS97 3.0 402.6 1.0 CG A:HIS117 3.1 476.4 1.0 NE2 A:HIS114 3.2 386.3 1.0 CD2 A:HIS114 3.3 369.9 1.0 CB A:HIS114 3.4 319.3 1.0 NE2 A:HIS117 3.4 486.4 1.0 CD2 A:HIS117 3.7 484.9 1.0 CA A:HIS114 3.8 321.8 1.0 CB A:HIS117 3.9 470.7 1.0 OG1 A:THR102 4.1 411.0 1.0 CB A:ASP100 4.1 501.5 1.0 O A:SER113 4.2 396.9 1.0 C A:SER113 4.3 385.3 1.0 N A:HIS114 4.4 346.9 1.0 CA A:CYS97 4.5 386.3 1.0 N A:ASP100 4.8 461.1 1.0 CB A:SER113 4.9 360.5 1.0 C A:CYS97 5.0 386.9 1.0

Zinc binding site 5 out of 16 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 5 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:606.1 occ:1.00 SG B:CYS17 2.1 623.4 1.0 SG B:CYS37 2.2 507.6 1.0 SG B:CYS14 2.3 528.4 1.0 SG B:CYS34 2.3 519.9 1.0 CB B:CYS17 2.6 527.1 1.0 CB B:CYS34 2.9 488.4 1.0 CB B:CYS14 2.9 472.9 1.0 CB B:CYS37 3.2 451.8 1.0 N B:CYS17 3.7 486.6 1.0 CA B:CYS17 3.7 497.6 1.0 NE2 B:GLN19 4.0 422.2 1.0 CD B:GLN19 4.1 419.8 1.0 OE1 B:GLN19 4.2 414.3 1.0 N B:LEU18 4.2 496.8 1.0 CA B:CYS34 4.3 474.1 1.0 CE2 B:PHE21 4.3 448.5 1.0 CA B:CYS14 4.4 434.0 1.0 C B:CYS17 4.4 510.1 1.0 N B:CYS34 4.6 474.9 1.0 CA B:CYS37 4.6 466.6 1.0 CZ B:PHE21 4.6 445.4 1.0 CE1 B:PHE33 4.7 430.0 1.0 C B:LEU16 4.7 462.4 1.0 CG B:GLN19 4.8 425.3 1.0 NH1 B:ARG35 4.8 467.5 1.0 CD1 B:PHE33 4.9 420.4 1.0 N B:CYS37 5.0 475.2 1.0 CB B:LEU16 5.0 433.1 1.0

Zinc binding site 6 out of 16 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 6 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:580.9 occ:1.00 CE1 B:HIS31 1.2 580.9 1.0 ND1 B:HIS31 1.9 571.2 1.0 SG B:CYS29 2.2 574.1 1.0 NE2 B:HIS31 2.3 584.8 1.0 SG B:CYS53 2.5 558.5 1.0 SG B:CYS56 2.6 653.6 1.0 OG B:SER55 2.7 518.7 1.0 CB B:CYS56 2.9 598.8 1.0 CG B:HIS31 3.0 564.6 1.0 CD2 B:HIS31 3.2 582.0 1.0 CB B:CYS29 3.5 504.2 1.0 N B:CYS56 3.6 547.1 1.0 CA B:CYS56 3.8 577.6 1.0 CB B:CYS53 3.9 545.5 1.0 CB B:SER55 4.1 497.7 1.0 CB B:HIS31 4.3 543.6 1.0 C B:SER55 4.5 486.3 1.0 C B:CYS56 4.7 601.7 1.0 CA B:SER55 4.7 466.9 1.0 CA B:CYS29 4.9 481.5 1.0 O B:CYS29 4.9 498.6 1.0 N B:SER55 5.0 443.9 1.0

Zinc binding site 7 out of 16 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 7 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:707.4 occ:1.00 ND1 B:HIS89 2.0 565.8 1.0 SG B:CYS105 2.2 697.0 1.0 SG B:CYS108 2.3 465.3 1.0 CE1 B:HIS89 2.4 549.8 1.0 SG B:CYS86 2.4 644.0 1.0 CB B:CYS108 2.9 491.8 1.0 CG B:HIS89 3.2 553.4 1.0 N B:CYS108 3.4 510.8 1.0 NE2 B:HIS89 3.5 547.2 1.0 CA B:CYS108 3.6 483.0 1.0 CB B:CYS105 3.8 605.6 1.0 CD2 B:HIS89 3.9 552.6 1.0 CB B:CYS86 4.0 540.4 1.0 CB B:HIS89 4.0 542.0 1.0 O B:ASP91 4.4 500.2 1.0 C B:VAL107 4.4 515.6 1.0 CB B:VAL107 4.5 512.3 1.0 N B:HIS89 4.5 593.3 1.0 OE1 B:GLU88 4.6 508.4 1.0 CB B:GLU88 4.7 556.7 1.0 CB B:ASP91 4.7 511.8 1.0 CA B:CYS105 4.8 592.2 1.0 O B:CYS105 4.9 583.9 1.0 CA B:VAL107 4.9 515.0 1.0 CA B:HIS89 4.9 561.8 1.0 C B:CYS105 5.0 566.7 1.0 N B:VAL107 5.0 515.6 1.0 CD B:GLU88 5.0 525.9 1.0

Zinc binding site 8 out of 16 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 8 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:595.9 occ:1.00 ND1 B:HIS114 1.9 435.7 1.0 ND1 B:HIS117 2.0 491.8 1.0 OD2 B:ASP100 2.0 633.0 1.0 CE1 B:HIS117 2.3 491.1 1.0 SG B:CYS97 2.3 478.9 1.0 CE1 B:HIS114 2.5 439.0 1.0 CG B:ASP100 2.6 653.6 1.0 CG B:HIS114 2.6 417.6 1.0 CG B:HIS117 3.1 484.3 1.0 CB B:HIS114 3.2 418.9 1.0 OD1 B:ASP100 3.3 665.7 1.0 NE2 B:HIS114 3.3 423.8 1.0 CD2 B:HIS114 3.4 415.5 1.0 CB B:CYS97 3.4 466.4 1.0 NE2 B:HIS117 3.4 486.2 1.0 CB B:ASP100 3.4 681.0 1.0 CA B:HIS114 3.5 422.3 1.0 CD2 B:HIS117 3.8 477.7 1.0 O B:SER113 3.9 426.6 1.0 CB B:HIS117 4.0 485.3 1.0 C B:SER113 4.1 427.1 1.0 N B:HIS114 4.2 425.7 1.0 N B:ASP100 4.3 642.0 1.0 CA B:ASP100 4.5 666.9 1.0 CA B:CYS97 4.7 444.2 1.0 C B:HIS114 4.7 423.2 1.0 CB B:SER113 5.0 427.2 1.0

Zinc binding site 9 out of 16 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 9 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:566.9 occ:1.00 SG C:CYS37 2.1 603.5 1.0 SG C:CYS17 2.3 517.6 1.0 CB C:CYS37 2.3 510.0 1.0 SG C:CYS14 2.3 487.4 1.0 SG C:CYS34 2.4 509.4 1.0 CB C:CYS34 2.7 467.7 1.0 CB C:CYS14 3.2 379.7 1.0 CA C:CYS37 3.7 500.0 1.0 CB C:CYS17 3.9 462.9 1.0 N C:CYS37 4.0 510.9 1.0 CA C:CYS34 4.1 489.9 1.0 N C:LEU18 4.2 438.0 1.0 N C:CYS17 4.3 430.2 1.0 N C:CYS34 4.3 528.5 1.0 CE1 C:PHE21 4.5 427.9 1.0 CA C:CYS17 4.6 451.0 1.0 CA C:CYS14 4.6 364.9 1.0 C C:CYS37 4.6 506.2 1.0 N C:LEU38 4.7 545.2 1.0 CD1 C:PHE33 4.8 455.0 1.0 C C:CYS34 4.8 503.0 1.0 CZ C:PHE21 4.8 425.2 1.0 C C:CYS17 4.9 462.2 1.0

Zinc binding site 10 out of 16 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 10 of Trim E3 Ubiquitin Ligase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:522.1 occ:1.00 CE1 C:HIS31 1.2 442.1 1.0 ND1 C:HIS31 2.0 385.0 1.0 NE2 C:HIS31 2.3 441.8 1.0 SG C:CYS29 2.4 442.0 1.0 SG C:CYS56 2.5 517.7 1.0 SG C:CYS53 2.5 482.3 1.0 OG C:SER55 2.7 484.4 1.0 CB C:CYS56 2.8 364.3 1.0 CG C:HIS31 3.2 352.8 1.0 CD2 C:HIS31 3.3 388.4 1.0 N C:CYS56 3.5 388.9 1.0 CB C:CYS29 3.6 422.2 1.0 CA C:CYS56 3.8 378.2 1.0 CB C:CYS53 3.9 448.4 1.0 CB C:SER55 4.1 451.5 1.0 C C:SER55 4.4 393.3 1.0 CB C:HIS31 4.5 344.3 1.0 C C:CYS56 4.6 408.4 1.0 O C:ALA58 4.7 438.6 1.0 CA C:SER55 4.7 425.2 1.0 CA C:CYS29 4.9 414.4 1.0 N C:SER55 4.9 423.2 1.0

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