Zinc in PDB 8eaz: Hoil-1/E2-Ub/Ub Transthiolation Complex

The structure of Hoil-1/E2-Ub/Ub Transthiolation Complex, PDB code: 8eaz was solved by X.S.Wang, T.R.Cotton, B.C.Lechtenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.74 / 3.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.953, 95.478, 115.006, 90, 110.58, 90
R / Rfree (%)	23.2 / 26.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Hoil-1/E2-Ub/Ub Transthiolation Complex (pdb code 8eaz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Hoil-1/E2-Ub/Ub Transthiolation Complex, PDB code: 8eaz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:125.6 occ:1.00 SG A:CYS308 2.3 123.6 1.0 SG A:CYS285 2.3 159.2 1.0 SG A:CYS305 2.3 132.6 1.0 SG A:CYS282 2.3 131.3 1.0 CB A:CYS308 3.0 114.0 1.0 CB A:CYS285 3.1 122.0 1.0 CB A:CYS305 3.3 130.7 1.0 CB A:CYS282 3.4 125.3 1.0 N A:CYS285 3.7 123.4 1.0 CA A:CYS285 4.0 128.1 1.0 CA A:CYS308 4.2 121.5 1.0 N A:CYS308 4.2 137.9 1.0 N A:CYS305 4.2 112.1 1.0 CA A:CYS305 4.3 120.1 1.0 C A:VAL284 4.6 121.6 1.0 CB A:VAL284 4.6 113.5 1.0 CA A:CYS282 4.7 128.1 1.0 C A:CYS285 4.8 136.6 1.0 O A:CYS282 4.9 126.6 1.0 N A:VAL284 4.9 131.0 1.0 CA A:VAL284 4.9 121.3 1.0 C A:CYS282 5.0 122.7 1.0

Zinc binding site 2 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:118.2 occ:1.00 ND1 A:HIS302 2.1 96.4 1.0 SG A:CYS323 2.3 102.8 1.0 SG A:CYS300 2.3 113.9 1.0 SG A:CYS332 2.3 108.0 1.0 CE1 A:HIS302 2.9 96.8 1.0 CB A:CYS300 3.0 116.0 1.0 CG A:HIS302 3.1 104.6 1.0 CB A:CYS323 3.2 91.2 1.0 CB A:CYS332 3.4 113.3 1.0 CB A:HIS302 3.6 110.3 1.0 NE2 A:HIS302 4.0 98.3 1.0 CB A:PHE325 4.1 104.3 1.0 CD2 A:HIS302 4.2 104.0 1.0 CA A:CYS300 4.4 97.4 1.0 CA A:CYS323 4.7 98.3 1.0 CD1 A:LEU297 4.7 113.0 1.0 C A:CYS300 4.7 99.1 1.0 N A:GLY334 4.7 99.2 1.0 O A:CYS300 4.8 99.8 1.0 CA A:CYS332 4.8 108.0 1.0 CG A:PHE325 4.8 102.7 1.0 N A:HIS302 4.8 99.8 1.0 CA A:HIS302 4.8 105.3 1.0 CA A:GLY334 4.8 99.1 1.0 CD2 A:PHE325 4.9 106.8 1.0 CE2 A:PHE304 5.0 112.0 1.0

Zinc binding site 3 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:93.5 occ:1.00 SG A:CYS371 2.3 91.3 1.0 SG A:CYS391 2.3 99.1 1.0 SG A:CYS376 2.3 91.8 1.0 SG A:CYS394 2.3 128.3 1.0 CB A:CYS391 3.1 92.4 1.0 CB A:CYS371 3.2 88.6 1.0 CB A:CYS376 3.5 100.4 1.0 CB A:CYS394 3.6 105.9 1.0 N A:CYS394 3.9 97.8 1.0 CB A:THR373 4.2 95.7 1.0 CA A:CYS394 4.3 105.4 1.0 OG1 A:THR373 4.4 97.2 1.0 CB A:VAL393 4.5 93.8 1.0 CA A:CYS391 4.6 92.5 1.0 CA A:CYS371 4.7 87.8 1.0 CG2 A:THR373 4.7 97.3 1.0 C A:VAL393 4.8 104.0 1.0 ND2 A:ASN398 4.9 102.1 1.0 CA A:CYS376 4.9 100.1 1.0 N A:VAL393 4.9 107.7 1.0 N A:GLY378 5.0 87.3 1.0 CA A:VAL393 5.0 104.3 1.0 O A:GLY378 5.0 90.9 1.0

Zinc binding site 4 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:106.6 occ:1.00 NE2 A:HIS406 2.1 99.4 1.0 SG A:CYS399 2.3 106.6 1.0 SG A:CYS402 2.3 109.2 1.0 SG A:CYS411 2.3 92.2 1.0 CD2 A:HIS406 2.9 101.0 1.0 CE1 A:HIS406 3.1 111.7 1.0 CB A:CYS399 3.3 103.7 1.0 CB A:CYS411 3.7 115.4 1.0 CB A:CYS402 3.8 100.2 1.0 CG A:HIS406 4.0 119.4 1.0 CA A:CYS411 4.1 119.3 1.0 ND1 A:HIS406 4.1 110.3 1.0 N A:CYS402 4.1 109.5 1.0 CA A:CYS402 4.5 110.5 1.0 N A:CYS411 4.6 114.0 1.0 CA A:CYS399 4.7 104.5 1.0 CB A:LEU401 4.8 104.5 1.0 O A:ALA404 4.9 109.0 1.0

Zinc binding site 5 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:72.0 occ:1.00 SG A:CYS450 2.3 67.2 1.0 SG A:CYS447 2.3 77.2 1.0 SG A:CYS468 2.3 84.3 1.0 SG A:CYS465 2.3 56.9 1.0 CB A:CYS465 3.3 59.8 1.0 CB A:CYS447 3.4 73.9 1.0 CB A:CYS450 3.4 80.0 1.0 CB A:CYS468 3.6 68.3 1.0 N A:CYS450 3.8 65.9 1.0 N A:CYS468 3.9 85.7 1.0 CA A:CYS450 4.2 76.8 1.0 CA A:CYS468 4.3 80.8 1.0 CG2 A:ILE452 4.4 55.6 1.0 CB A:VAL467 4.5 76.3 1.0 CB A:GLN449 4.7 72.0 1.0 OG1 A:THR470 4.7 59.1 1.0 CA A:CYS465 4.7 68.7 1.0 CB A:THR470 4.8 58.6 1.0 CA A:CYS447 4.8 74.2 1.0 C A:VAL467 4.8 78.1 1.0 C A:CYS450 4.8 72.7 1.0 C A:CYS468 4.9 69.3 1.0 C A:GLN449 4.9 70.4 1.0 CG1 A:VAL467 5.0 78.7 1.0 N A:GLN451 5.0 67.6 1.0

Zinc binding site 6 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:76.9 occ:1.00 SG A:CYS473 2.3 61.4 1.0 SG A:CYS502 2.3 76.6 1.0 SG A:CYS493 2.3 76.5 1.0 SG A:CYS509 2.3 77.6 1.0 ZN A:ZN1007 2.8 64.2 1.0 CB A:CYS502 3.3 91.7 1.0 CB A:CYS493 3.4 75.6 1.0 CB A:CYS473 3.4 74.9 1.0 CB A:CYS509 3.7 77.4 1.0 CB A:CYS495 3.9 79.5 1.0 CD A:ARG480 4.3 77.5 1.0 CG2 A:THR476 4.3 81.6 1.0 OG1 A:THR476 4.3 67.5 1.0 SG A:CYS495 4.4 84.7 1.0 CA A:CYS473 4.5 58.8 1.0 SG A:CYS506 4.6 78.4 1.0 NE A:ARG480 4.7 78.8 1.0 CA A:CYS502 4.8 82.3 1.0 CA A:CYS493 4.8 82.3 1.0 CA A:CYS495 5.0 84.5 1.0 CB A:THR476 5.0 71.4 1.0

Zinc binding site 7 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:64.2 occ:1.00 SG A:CYS506 2.3 78.4 1.0 SG A:CYS502 2.3 76.6 1.0 SG A:CYS509 2.3 77.6 1.0 SG A:CYS495 2.3 84.7 1.0 ZN A:ZN1006 2.8 76.9 1.0 CB A:CYS495 3.0 79.5 1.0 CB A:CYS506 3.4 77.7 1.0 CB A:CYS502 3.5 91.7 1.0 CB A:CYS509 3.7 77.4 1.0 N A:CYS502 3.9 78.7 1.0 N A:CYS509 4.3 80.8 1.0 CA A:CYS502 4.3 82.3 1.0 CA A:CYS495 4.4 84.5 1.0 SG A:CYS493 4.4 76.5 1.0 CA A:CYS509 4.6 78.5 1.0 SG A:CYS473 4.6 61.4 1.0 CA A:CYS506 4.8 78.0 1.0 N A:HIS503 4.9 79.2 1.0 C A:PRO501 5.0 79.5 1.0

Zinc binding site 8 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:138.4 occ:1.00 SG B:CYS308 2.3 150.2 1.0 SG B:CYS305 2.3 147.1 1.0 SG B:CYS285 2.3 135.2 1.0 SG B:CYS282 2.3 144.8 1.0 CB B:CYS305 3.1 152.2 1.0 CB B:CYS308 3.2 142.0 1.0 CB B:CYS282 3.3 132.8 1.0 CB B:CYS285 3.3 143.2 1.0 N B:CYS285 3.8 143.0 1.0 N B:CYS305 4.0 141.3 1.0 CA B:CYS305 4.1 142.8 1.0 N B:CYS308 4.2 134.4 1.0 CA B:CYS285 4.2 150.4 1.0 CA B:CYS308 4.3 132.5 1.0 CB B:VAL284 4.6 134.1 1.0 CA B:CYS282 4.7 138.5 1.0 C B:VAL284 4.7 142.0 1.0 C B:CYS305 4.8 150.4 1.0 N B:VAL284 4.9 130.4 1.0 C B:CYS282 5.0 141.7 1.0 O B:CYS282 5.0 146.1 1.0 CA B:VAL284 5.0 142.4 1.0

Zinc binding site 9 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:113.4 occ:1.00 ND1 B:HIS302 2.1 102.8 1.0 SG B:CYS323 2.3 108.0 1.0 SG B:CYS300 2.3 133.0 1.0 SG B:CYS332 2.3 122.6 1.0 CE1 B:HIS302 2.9 104.9 1.0 CB B:CYS300 3.1 124.3 1.0 CG B:HIS302 3.2 119.2 1.0 CB B:CYS323 3.2 108.0 1.0 CB B:CYS332 3.5 125.2 1.0 CB B:HIS302 3.6 119.2 1.0 NE2 B:HIS302 4.1 124.8 1.0 CD2 B:HIS302 4.2 120.7 1.0 CB B:PHE325 4.3 121.5 1.0 CA B:CYS300 4.5 115.5 1.0 CD1 B:LEU297 4.5 119.6 1.0 N B:GLY334 4.6 114.5 1.0 CA B:CYS323 4.6 105.9 1.0 CA B:GLY334 4.7 107.3 1.0 C B:CYS300 4.8 118.4 1.0 O B:CYS300 4.8 104.3 1.0 N B:HIS302 4.8 125.4 1.0 CA B:HIS302 4.9 125.8 1.0 CA B:CYS332 4.9 119.8 1.0 CZ B:PHE304 5.0 122.9 1.0 CE2 B:PHE304 5.0 134.5 1.0

Zinc binding site 10 out of 14 in the Hoil-1/E2-Ub/Ub Transthiolation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Hoil-1/E2-Ub/Ub Transthiolation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:79.1 occ:1.00 SG B:CYS371 2.3 86.5 1.0 SG B:CYS376 2.3 85.4 1.0 SG B:CYS391 2.3 92.9 1.0 SG B:CYS394 2.3 107.1 1.0 CB B:CYS391 3.1 86.0 1.0 CB B:CYS371 3.2 96.6 1.0 CB B:CYS376 3.5 100.7 1.0 CB B:CYS394 3.5 90.0 1.0 N B:CYS394 3.9 95.6 1.0 CB B:THR373 4.2 89.1 1.0 CA B:CYS394 4.3 92.4 1.0 OG1 B:THR373 4.5 90.4 1.0 CA B:CYS391 4.6 87.2 1.0 CB B:VAL393 4.6 91.0 1.0 CA B:CYS371 4.7 92.5 1.0 CG2 B:THR373 4.7 89.8 1.0 C B:VAL393 4.8 100.3 1.0 ND2 B:ASN398 4.9 85.4 1.0 N B:GLY378 4.9 81.8 1.0 CA B:CYS376 4.9 98.0 1.0 C B:CYS394 4.9 96.9 1.0 CA B:GLY378 4.9 81.9 1.0 N B:VAL393 5.0 100.5 1.0

X.S.Wang, T.R.Cotton, S.J.Trevelyan, L.W.Richardson, W.T.Lee, J.Silke, B.C.Lechtenberg. The Unifying Catalytic Mechanism of the Ring-Between-Ring E3 Ubiquitin Ligase Family. Nat Commun V. 14 168 2023.
ISSN: ESSN 2041-1723
PubMed: 36631489
DOI: 10.1038/S41467-023-35871-Z