Zinc in PDB 9egv: Hoil-1 RING2 Domain Bound to Ubiquitin

All present enzymatic activity of Hoil-1 RING2 Domain Bound to Ubiquitin:
2.3.2.31;

The structure of Hoil-1 RING2 Domain Bound to Ubiquitin, PDB code: 9egv was solved by X.S.Wang, B.C.Lechtenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.00
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.922, 95.922, 187.429, 90, 90, 90
R / Rfree (%)	18 / 20.8

The structure of Hoil-1 RING2 Domain Bound to Ubiquitin also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Hoil-1 RING2 Domain Bound to Ubiquitin (pdb code 9egv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Hoil-1 RING2 Domain Bound to Ubiquitin, PDB code: 9egv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Hoil-1 RING2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hoil-1 RING2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:29.5 occ:1.00 SG A:CYS468 2.3 30.6 1.0 SG A:CYS465 2.3 33.2 1.0 SG A:CYS450 2.3 32.0 1.0 SG A:CYS447 2.4 30.9 1.0 H A:CYS450 3.0 38.8 1.0 HB3 A:CYS450 3.1 43.6 1.0 HB3 A:CYS465 3.1 38.0 1.0 CB A:CYS465 3.2 31.6 1.0 HB3 A:CYS447 3.2 39.3 1.0 H A:CYS468 3.2 40.4 1.0 CB A:CYS447 3.2 32.8 1.0 HB2 A:CYS447 3.2 39.3 1.0 HB2 A:CYS465 3.3 38.0 1.0 CB A:CYS450 3.3 36.4 1.0 HB3 A:CYS468 3.3 40.4 1.0 CB A:CYS468 3.4 33.7 1.0 HB A:VAL467 3.5 42.3 1.0 HB3 A:GLN449 3.7 36.0 1.0 N A:CYS450 3.7 32.4 1.0 N A:CYS468 3.8 33.7 1.0 HG22 A:ILE452 4.0 39.8 1.0 HB2 A:CYS450 4.1 43.6 1.0 CA A:CYS450 4.1 33.5 1.0 HB A:THR470 4.2 35.9 1.0 HB2 A:CYS468 4.2 40.4 1.0 CA A:CYS468 4.2 33.2 1.0 H A:VAL467 4.3 41.8 1.0 H A:THR470 4.4 35.6 1.0 HG21 A:ILE452 4.4 39.8 1.0 CB A:VAL467 4.4 35.2 1.0 H A:GLN449 4.4 34.9 1.0 H A:GLN451 4.5 40.9 1.0 HG1 A:THR470 4.5 41.1 1.0 HG12 A:VAL467 4.6 43.2 1.0 H A:ILE452 4.6 38.6 1.0 CA A:CYS465 4.6 30.6 1.0 CG2 A:ILE452 4.7 33.1 1.0 CA A:CYS447 4.7 29.3 1.0 CB A:GLN449 4.7 30.0 1.0 HD11 A:ILE472 4.7 36.5 1.0 H A:HIS469 4.7 38.8 1.0 C A:CYS450 4.8 34.3 1.0 C A:VAL467 4.8 36.7 1.0 C A:GLN449 4.8 35.4 1.0 N A:GLN451 4.9 34.1 1.0 C A:CYS468 4.9 33.4 1.0 N A:VAL467 4.9 34.8 1.0 HA A:CYS450 4.9 40.2 1.0 HA A:CYS465 4.9 36.8 1.0 OG1 A:THR470 4.9 34.3 1.0 CA A:VAL467 4.9 35.6 1.0 CG1 A:VAL467 5.0 36.0 1.0 CB A:THR470 5.0 29.9 1.0 HA A:CYS447 5.0 35.1 1.0

Zinc binding site 2 out of 6 in the Hoil-1 RING2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hoil-1 RING2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:25.8 occ:1.00 SG A:CYS473 2.4 25.5 1.0 SG A:CYS493 2.4 23.9 1.0 SG A:CYS509 2.4 25.8 1.0 SG A:CYS502 2.4 25.2 1.0 HB2 A:CYS495 3.0 34.6 1.0 HB2 A:CYS473 3.0 32.7 1.0 HB2 A:CYS509 3.2 30.8 1.0 ZN A:ZN603 3.2 27.5 1.0 HB2 A:CYS493 3.2 31.4 1.0 HB3 A:CYS502 3.2 32.3 1.0 CB A:CYS509 3.3 25.7 1.0 CB A:CYS493 3.3 26.1 1.0 CB A:CYS473 3.3 27.3 1.0 CB A:CYS502 3.3 26.9 1.0 HB3 A:CYS509 3.4 30.8 1.0 HB2 A:CYS502 3.4 32.3 1.0 HB3 A:CYS493 3.5 31.4 1.0 HG1 A:THR476 3.7 33.3 1.0 HG12 A:VAL475 3.8 34.6 1.0 HB3 A:CYS473 3.8 32.7 1.0 HD3 A:ARG480 3.9 32.2 1.0 HD2 A:ARG480 3.9 32.2 1.0 CB A:CYS495 4.0 28.9 1.0 HG23 A:THR476 4.0 35.7 1.0 HG13 A:VAL475 4.2 34.6 1.0 CD A:ARG480 4.3 26.8 1.0 HB3 A:CYS495 4.3 34.6 1.0 H A:CYS495 4.3 30.2 1.0 CG1 A:VAL475 4.4 28.9 1.0 OG1 A:THR476 4.4 27.7 1.0 HA A:CYS473 4.4 28.6 1.0 HG21 A:THR476 4.4 35.7 1.0 HG11 A:VAL475 4.5 34.6 1.0 CA A:CYS473 4.5 23.9 1.0 CG2 A:THR476 4.6 29.7 1.0 H A:THR476 4.6 33.6 1.0 NE A:ARG480 4.6 24.6 1.0 SG A:CYS495 4.7 28.9 1.0 HA A:ARG480 4.7 28.4 1.0 CA A:CYS493 4.7 26.4 1.0 CA A:CYS509 4.7 28.6 1.0 CA A:CYS502 4.8 27.9 1.0 H A:CYS502 4.8 34.5 1.0 HE A:ARG480 4.8 29.5 1.0 O A:CYS509 4.8 31.1 1.0 SG A:CYS506 4.9 27.3 1.0 N A:CYS495 4.9 25.2 1.0 CA A:CYS495 5.0 27.4 1.0

Zinc binding site 3 out of 6 in the Hoil-1 RING2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hoil-1 RING2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:27.5 occ:1.00 SG A:CYS506 2.3 27.3 1.0 SG A:CYS495 2.4 28.9 1.0 SG A:CYS509 2.4 25.8 1.0 SG A:CYS502 2.4 25.2 1.0 HB2 A:CYS495 2.8 34.6 1.0 CB A:CYS495 3.1 28.9 1.0 ZN A:ZN602 3.2 25.8 1.0 H A:CYS502 3.2 34.5 1.0 HB3 A:CYS509 3.2 30.8 1.0 HB2 A:CYS506 3.2 30.9 1.0 CB A:CYS506 3.2 25.8 1.0 HB3 A:CYS506 3.3 30.9 1.0 CB A:CYS509 3.4 25.7 1.0 H A:CYS509 3.5 36.1 1.0 HB3 A:CYS502 3.5 32.3 1.0 HB3 A:CYS495 3.6 34.6 1.0 CB A:CYS502 3.6 26.9 1.0 O A:HOH703 3.7 38.3 1.0 N A:CYS502 4.0 28.7 1.0 HH12 A:ARG496 4.0 47.5 1.0 HG11 A:VAL475 4.0 34.6 1.0 N A:CYS509 4.1 30.1 1.0 HB2 A:CYS509 4.1 30.8 1.0 CA A:CYS502 4.4 27.9 1.0 HG12 A:VAL475 4.4 34.6 1.0 CA A:CYS509 4.4 28.6 1.0 HB2 A:CYS502 4.4 32.3 1.0 HA A:CYS495 4.4 32.9 1.0 CA A:CYS495 4.4 27.4 1.0 H A:HIS503 4.5 31.8 1.0 CG1 A:VAL475 4.6 28.9 1.0 NH1 A:ARG496 4.6 39.6 1.0 CA A:CYS506 4.7 29.7 1.0 HB3 A:PRO501 4.7 35.9 1.0 HG13 A:VAL475 4.7 34.6 1.0 HH11 A:ARG496 4.7 47.5 1.0 HA A:PRO501 4.8 33.7 1.0 SG A:CYS493 4.8 23.9 1.0 HA A:CYS506 4.9 35.7 1.0 SG A:CYS473 4.9 25.5 1.0 N A:HIS503 4.9 26.5 1.0 C A:CYS502 5.0 30.7 1.0

Zinc binding site 4 out of 6 in the Hoil-1 RING2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hoil-1 RING2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:29.9 occ:1.00 SG B:CYS465 2.3 30.5 1.0 SG B:CYS447 2.3 31.5 1.0 SG B:CYS450 2.3 27.9 1.0 SG B:CYS468 2.4 29.5 1.0 H B:CYS450 3.0 46.7 1.0 HB3 B:CYS450 3.0 36.7 1.0 H B:CYS468 3.0 37.2 1.0 HB3 B:CYS468 3.1 37.1 1.0 CB B:CYS447 3.2 34.9 1.0 HB3 B:CYS447 3.2 41.8 1.0 HB2 B:CYS447 3.2 41.8 1.0 HB3 B:CYS465 3.2 38.1 1.0 CB B:CYS465 3.2 31.8 1.0 CB B:CYS450 3.2 30.6 1.0 HB2 B:CYS465 3.3 38.1 1.0 CB B:CYS468 3.3 30.9 1.0 N B:CYS450 3.7 38.9 1.0 HB3 B:GLN449 3.7 44.1 1.0 HG22 B:THR470 3.7 43.1 1.0 HB B:VAL467 3.7 42.0 1.0 N B:CYS468 3.8 31.0 1.0 HG21 B:THR470 3.9 43.1 1.0 HG22 B:ILE452 4.0 39.4 1.0 CA B:CYS450 4.0 33.0 1.0 HB2 B:CYS450 4.0 36.7 1.0 CA B:CYS468 4.1 33.9 1.0 HB2 B:CYS468 4.1 37.1 1.0 HG21 B:ILE452 4.3 39.4 1.0 CG2 B:THR470 4.3 36.0 1.0 H B:THR470 4.3 34.2 1.0 H B:GLN449 4.3 41.1 1.0 H B:VAL467 4.5 41.8 1.0 H B:GLN451 4.5 36.7 1.0 H B:ILE452 4.5 36.8 1.0 CG2 B:ILE452 4.6 32.8 1.0 H B:HIS469 4.6 38.7 1.0 CA B:CYS447 4.6 33.9 1.0 HD11 B:ILE472 4.6 40.1 1.0 CB B:GLN449 4.7 36.8 1.0 CB B:VAL467 4.7 35.0 1.0 CA B:CYS465 4.7 32.7 1.0 C B:CYS450 4.7 36.5 1.0 HG12 B:VAL467 4.8 42.3 1.0 C B:CYS468 4.8 33.6 1.0 HB B:THR470 4.8 42.9 1.0 C B:GLN449 4.8 35.9 1.0 HB B:ILE452 4.8 42.6 1.0 C B:VAL467 4.9 34.0 1.0 HA B:CYS450 4.9 39.6 1.0 N B:GLN451 4.9 30.6 1.0 HA B:CYS447 4.9 40.6 1.0 N B:HIS469 4.9 32.2 1.0 HA B:CYS468 4.9 40.7 1.0 HA B:CYS465 5.0 39.2 1.0 N B:GLN449 5.0 34.2 1.0 HG23 B:THR470 5.0 43.1 1.0

Zinc binding site 5 out of 6 in the Hoil-1 RING2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hoil-1 RING2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:29.4 occ:1.00 SG B:CYS493 2.3 28.5 1.0 SG B:CYS473 2.3 30.4 1.0 SG B:CYS509 2.3 29.2 1.0 SG B:CYS502 2.5 28.3 1.0 HB2 B:CYS473 3.0 38.0 1.0 HB2 B:CYS495 3.2 34.7 1.0 ZN B:ZN603 3.2 31.1 1.0 HB2 B:CYS493 3.2 39.6 1.0 CB B:CYS493 3.2 33.0 1.0 HB3 B:CYS502 3.2 35.2 1.0 CB B:CYS473 3.3 31.6 1.0 HB2 B:CYS509 3.3 40.9 1.0 CB B:CYS509 3.3 34.1 1.0 CB B:CYS502 3.3 29.4 1.0 HB2 B:CYS502 3.4 35.2 1.0 HB3 B:CYS493 3.4 39.6 1.0 HB3 B:CYS509 3.4 40.9 1.0 HD3 B:ARG480 3.7 34.6 1.0 HD2 B:ARG480 3.8 34.6 1.0 HG12 B:VAL475 3.8 42.0 1.0 HG1 B:THR476 3.8 40.6 1.0 HG23 B:THR476 3.8 42.9 1.0 HB3 B:CYS473 3.8 38.0 1.0 CB B:CYS495 4.1 28.9 1.0 CD B:ARG480 4.2 28.8 1.0 HG13 B:VAL475 4.2 42.0 1.0 HG21 B:THR476 4.2 42.9 1.0 CG1 B:VAL475 4.3 35.0 1.0 OG1 B:THR476 4.4 33.8 1.0 HA B:CYS473 4.4 40.1 1.0 HB3 B:CYS495 4.4 34.7 1.0 H B:CYS495 4.4 35.4 1.0 HG11 B:VAL475 4.4 42.0 1.0 CG2 B:THR476 4.4 35.8 1.0 CA B:CYS473 4.5 33.5 1.0 NE B:ARG480 4.5 26.7 1.0 H B:THR476 4.6 37.8 1.0 HA B:ARG480 4.7 31.9 1.0 SG B:CYS495 4.7 31.3 1.0 CA B:CYS493 4.7 30.8 1.0 HE B:ARG480 4.8 32.0 1.0 CA B:CYS509 4.8 37.5 1.0 SG B:CYS506 4.8 32.1 1.0 CA B:CYS502 4.8 30.8 1.0 H B:CYS502 4.9 35.9 1.0 H B:CYS493 4.9 31.8 1.0 HH11 B:ARG480 5.0 31.3 1.0

Zinc binding site 6 out of 6 in the Hoil-1 RING2 Domain Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hoil-1 RING2 Domain Bound to Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:31.1 occ:1.00 SG B:CYS506 2.3 32.1 1.0 SG B:CYS495 2.4 31.3 1.0 SG B:CYS502 2.4 28.3 1.0 SG B:CYS509 2.4 29.2 1.0 HB2 B:CYS495 2.8 34.7 1.0 H B:CYS502 3.1 35.9 1.0 HB3 B:CYS509 3.1 40.9 1.0 ZN B:ZN602 3.2 29.4 1.0 CB B:CYS495 3.2 28.9 1.0 CB B:CYS506 3.3 35.7 1.0 H B:CYS509 3.3 42.7 1.0 HB2 B:CYS506 3.3 42.9 1.0 HB3 B:CYS506 3.4 42.9 1.0 HB3 B:CYS502 3.4 35.2 1.0 CB B:CYS509 3.4 34.1 1.0 CB B:CYS502 3.5 29.4 1.0 HB3 B:CYS495 3.6 34.7 1.0 O B:HOH732 3.7 35.5 1.0 N B:CYS502 3.9 29.9 1.0 N B:CYS509 3.9 35.5 1.0 HG11 B:VAL475 4.0 42.0 1.0 HB2 B:CYS509 4.1 40.9 1.0 HB2 B:CYS502 4.3 35.2 1.0 CA B:CYS509 4.3 37.5 1.0 CA B:CYS502 4.3 30.8 1.0 HG12 B:VAL475 4.4 42.0 1.0 HA B:CYS495 4.5 36.7 1.0 CA B:CYS495 4.5 30.6 1.0 H B:HIS503 4.5 35.9 1.0 CG1 B:VAL475 4.6 35.0 1.0 HG13 B:VAL475 4.7 42.0 1.0 CA B:CYS506 4.7 39.4 1.0 HA B:PRO501 4.7 33.7 1.0 HB3 B:PRO501 4.7 37.4 1.0 SG B:CYS493 4.7 28.5 1.0 N B:HIS503 4.9 29.9 1.0 SG B:CYS473 4.9 30.4 1.0 HE B:ARG496 4.9 62.5 1.0 HA B:CYS506 4.9 47.3 1.0 HA B:ASN508 4.9 50.8 1.0 C B:CYS502 5.0 34.1 1.0 C B:ASN508 5.0 35.3 1.0

X.S.Wang, J.Jiou, A.Cerra, S.A.Cobbold, M.Jochem, K.H.T.Mak, L.Corcilius, R.J.Payne, E.D.Goddard-Borger, D.Komander, B.C.Lechtenberg. The Rbr E3 Ubiquitin Ligase Hoil-1 Can Ubiquitinate Diverse Non-Protein Substrates in Vitro Biorxiv 2024.
ISSN: ISSN 2692-8205