Zinc in PDB 5o6t: BIRC4 Ring in Complex with Dimeric Ubiquitin Variant

All present enzymatic activity of BIRC4 Ring in Complex with Dimeric Ubiquitin Variant:
2.3.2.27;

The structure of BIRC4 Ring in Complex with Dimeric Ubiquitin Variant, PDB code: 5o6t was solved by M.Gabrielsen, L.Buetow, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.18 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.715, 69.972, 109.747, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.3

The binding sites of Zinc atom in the BIRC4 Ring in Complex with Dimeric Ubiquitin Variant (pdb code 5o6t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the BIRC4 Ring in Complex with Dimeric Ubiquitin Variant, PDB code: 5o6t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the BIRC4 Ring in Complex with Dimeric Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BIRC4 Ring in Complex with Dimeric Ubiquitin Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.9 occ:1.00 SG A:CYS453 2.3 18.5 1.0 SG A:CYS474 2.3 19.6 1.0 SG A:CYS450 2.3 16.4 1.0 SG A:CYS471 2.4 16.4 1.0 HB2 A:CYS474 2.8 16.3 1.0 H A:CYS453 2.8 18.5 1.0 HB3 A:CYS450 3.0 14.1 1.0 H A:CYS471 3.0 14.2 1.0 HB3 A:CYS453 3.1 17.8 1.0 CB A:CYS450 3.1 13.6 1.0 CB A:CYS474 3.1 16.6 1.0 HB2 A:CYS450 3.2 15.1 1.0 CB A:CYS453 3.3 16.6 1.0 HH21 A:ARG456 3.3 27.2 1.0 HB3 A:CYS471 3.4 15.3 1.0 HB2 A:ARG456 3.5 18.8 1.0 H A:CYS474 3.5 17.4 1.0 CB A:CYS471 3.5 14.2 1.0 HE A:ARG456 3.6 24.8 1.0 HB A:ILE452 3.6 18.7 1.0 N A:CYS453 3.6 18.9 1.0 HB3 A:CYS474 3.8 17.6 1.0 NH2 A:ARG456 3.9 28.2 1.0 N A:CYS471 4.0 13.4 1.0 CA A:CYS453 4.0 17.1 1.0 H A:ARG456 4.1 19.1 1.0 NE A:ARG456 4.2 23.8 1.0 HB2 A:CYS453 4.2 15.0 1.0 H A:ILE452 4.2 15.8 1.0 N A:CYS474 4.3 17.1 1.0 CA A:CYS474 4.3 16.6 1.0 CA A:CYS471 4.3 12.9 1.0 HB2 A:CYS471 4.3 13.8 1.0 CZ A:ARG456 4.4 37.2 1.0 HH22 A:ARG456 4.5 28.9 1.0 H A:MET454 4.5 19.8 1.0 CA A:CYS450 4.5 14.3 1.0 HA A:THR470 4.5 15.4 1.0 CB A:ARG456 4.6 16.9 1.0 HG22 A:ILE452 4.6 20.8 1.0 HB A:THR470 4.6 19.7 1.0 CB A:ILE452 4.6 19.1 1.0 H A:ASP455 4.6 19.0 1.0 HB2 A:GLN473 4.7 20.1 1.0 C A:ILE452 4.7 20.2 1.0 HA A:CYS474 4.8 20.3 1.0 HA A:CYS453 4.8 17.0 1.0 O A:ARG456 4.9 19.3 1.0 C A:CYS453 4.9 20.9 1.0 N A:ILE452 4.9 16.7 1.0 C A:CYS471 4.9 15.8 1.0 N A:MET454 5.0 17.5 1.0 CA A:ILE452 5.0 16.1 1.0 HA A:CYS450 5.0 12.3 1.0

Zinc binding site 2 out of 4 in the BIRC4 Ring in Complex with Dimeric Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BIRC4 Ring in Complex with Dimeric Ubiquitin Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:16.7 occ:1.00 ND1 A:HIS467 2.0 19.1 1.0 SG A:CYS465 2.3 15.8 1.0 SG A:CYS481 2.3 17.1 1.0 SG A:CYS484 2.3 19.6 1.0 HB2 A:HIS467 2.9 10.6 1.0 HB2 A:CYS465 2.9 13.1 1.0 CE1 A:HIS467 2.9 19.6 1.0 HB3 A:CYS481 2.9 15.6 1.0 CB A:CYS481 3.0 15.7 1.0 CG A:HIS467 3.1 17.1 1.0 HB2 A:CYS481 3.1 16.4 1.0 H A:CYS484 3.1 18.0 0.6 HE1 A:HIS467 3.1 20.0 1.0 CB A:CYS465 3.2 14.5 1.0 H A:CYS484 3.2 18.5 0.4 HB2 A:MET483 3.5 24.9 0.6 HB3 A:CYS484 3.5 20.1 1.0 CB A:HIS467 3.5 14.1 1.0 H A:HIS467 3.5 16.2 1.0 CB A:CYS484 3.5 18.9 1.0 HB2 A:MET483 3.6 18.1 0.4 HB3 A:CYS465 3.6 15.8 1.0 HD2 A:PHE462 3.8 16.4 1.0 N A:CYS484 3.9 19.3 1.0 HB A:THR486 3.9 18.2 1.0 NE2 A:HIS467 4.1 20.2 1.0 H A:THR486 4.1 19.0 1.0 CD2 A:HIS467 4.2 19.4 1.0 H A:MET483 4.2 20.6 0.6 H A:MET483 4.2 17.9 0.4 HB3 A:HIS467 4.3 13.6 1.0 CA A:CYS484 4.3 19.2 1.0 N A:HIS467 4.3 13.4 1.0 HG1 A:THR486 4.3 24.6 1.0 O A:HOH1153 4.3 38.6 1.0 HB2 A:CYS484 4.4 17.8 1.0 CA A:HIS467 4.5 12.9 1.0 CA A:CYS481 4.5 15.9 1.0 CA A:CYS465 4.5 13.9 1.0 CB A:MET483 4.5 24.7 0.6 CB A:MET483 4.6 18.8 0.4 HG2 A:MET483 4.6 28.7 0.6 H A:TYR485 4.7 20.9 1.0 C A:CYS465 4.7 14.3 1.0 HB2 A:PHE462 4.7 12.3 1.0 C A:MET483 4.8 22.5 0.4 O A:CYS465 4.8 15.9 1.0 CB A:THR486 4.9 19.9 1.0 C A:MET483 4.9 24.2 0.6 HA A:CYS481 4.9 13.6 1.0 C A:CYS484 4.9 22.2 1.0 CD2 A:PHE462 4.9 15.6 1.0 OG1 A:THR486 5.0 23.6 1.0 HE2 A:HIS467 5.0 23.0 1.0 N A:MET483 5.0 20.9 0.6 N A:MET483 5.0 17.9 0.4 N A:TYR485 5.0 21.1 1.0

Zinc binding site 3 out of 4 in the BIRC4 Ring in Complex with Dimeric Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BIRC4 Ring in Complex with Dimeric Ubiquitin Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:17.1 occ:1.00 SG B:CYS453 2.3 18.6 1.0 SG B:CYS474 2.3 19.8 1.0 SG B:CYS471 2.3 16.7 1.0 SG B:CYS450 2.3 16.2 1.0 H B:CYS453 2.7 18.4 1.0 HB2 B:CYS474 2.8 19.2 1.0 HB3 B:CYS450 3.0 10.0 1.0 H B:CYS471 3.0 13.6 1.0 HB3 B:CYS453 3.0 18.1 1.0 CB B:CYS450 3.1 13.8 1.0 CB B:CYS474 3.2 17.4 1.0 HH21 B:ARG456 3.2 30.4 1.0 HB2 B:CYS450 3.2 15.4 1.0 CB B:CYS453 3.2 17.5 1.0 HB3 B:CYS471 3.4 13.8 1.0 CB B:CYS471 3.5 14.2 1.0 H B:CYS474 3.6 19.6 1.0 HB2 B:ARG456 3.6 17.2 1.0 N B:CYS453 3.7 18.3 1.0 HE B:ARG456 3.7 30.0 1.0 HB B:ILE452 3.7 20.1 1.0 NH2 B:ARG456 3.8 30.2 1.0 HB3 B:CYS474 3.8 18.8 1.0 N B:CYS471 4.0 14.9 1.0 CA B:CYS453 4.0 17.5 1.0 HB2 B:CYS453 4.1 18.6 1.0 H B:ARG456 4.2 17.6 1.0 NE B:ARG456 4.2 29.6 1.0 N B:CYS474 4.3 18.4 1.0 H B:ILE452 4.3 19.2 1.0 H B:ILE452 4.3 16.4 0.0 CA B:CYS474 4.3 17.9 1.0 CZ B:ARG456 4.3 41.8 1.0 HH22 B:ARG456 4.3 31.8 1.0 CA B:CYS471 4.3 14.2 1.0 HB2 B:CYS471 4.4 15.9 1.0 HG22 B:ILE452 4.5 21.9 1.0 HA B:THR470 4.5 11.4 1.0 CA B:CYS450 4.5 13.9 1.0 H B:MET454 4.6 17.4 1.0 HB2 B:GLN473 4.6 19.9 1.0 CB B:ARG456 4.7 15.8 1.0 CB B:ILE452 4.7 20.1 1.0 H B:ASP455 4.8 16.3 1.0 C B:ILE452 4.8 21.9 1.0 HA B:CYS474 4.8 18.5 1.0 HB B:THR470 4.8 15.7 1.0 HA B:CYS453 4.9 18.8 1.0 C B:CYS453 4.9 19.8 1.0 C B:CYS471 5.0 16.6 1.0 HA B:CYS450 5.0 14.1 1.0 C B:CYS450 5.0 17.2 1.0

Zinc binding site 4 out of 4 in the BIRC4 Ring in Complex with Dimeric Ubiquitin Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BIRC4 Ring in Complex with Dimeric Ubiquitin Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:16.5 occ:1.00 ND1 B:HIS467 2.0 18.1 1.0 SG B:CYS465 2.3 15.4 1.0 SG B:CYS484 2.3 18.9 1.0 SG B:CYS481 2.3 17.0 1.0 HB2 B:HIS467 2.8 13.6 1.0 HB3 B:CYS481 3.0 12.5 1.0 CE1 B:HIS467 3.0 20.4 1.0 HB2 B:CYS465 3.0 11.2 1.0 CB B:CYS481 3.0 15.3 1.0 CG B:HIS467 3.1 16.1 1.0 HB2 B:CYS481 3.1 15.5 1.0 H B:CYS484 3.1 19.4 1.0 HE1 B:HIS467 3.2 21.5 1.0 CB B:CYS465 3.2 14.2 1.0 HB3 B:CYS484 3.4 18.0 1.0 CB B:HIS467 3.4 14.2 1.0 HB2 B:MET483 3.5 25.1 1.0 CB B:CYS484 3.5 17.6 1.0 H B:HIS467 3.5 14.6 1.0 HB3 B:CYS465 3.6 13.7 1.0 HD2 B:PHE462 3.8 15.0 1.0 N B:CYS484 3.9 19.1 1.0 HB B:THR486 3.9 19.2 1.0 NE2 B:HIS467 4.1 20.4 1.0 H B:THR486 4.1 13.2 1.0 HB3 B:HIS467 4.2 14.9 1.0 CD2 B:HIS467 4.2 19.1 1.0 HG1 B:THR486 4.2 23.1 1.0 CA B:CYS484 4.3 18.4 1.0 H B:MET483 4.3 19.5 1.0 N B:HIS467 4.3 13.2 1.0 HB2 B:CYS484 4.4 17.5 1.0 O B:HOH644 4.4 33.4 1.0 CA B:HIS467 4.5 13.6 1.0 CB B:MET483 4.5 24.7 1.0 CA B:CYS481 4.5 15.5 1.0 CA B:CYS465 4.6 13.9 1.0 H B:TYR485 4.6 18.1 1.0 HB2 B:PHE462 4.7 15.3 1.0 C B:CYS465 4.8 15.1 1.0 HG2 B:MET483 4.8 31.2 1.0 CD2 B:PHE462 4.9 16.6 1.0 HG3 B:MET483 4.9 30.7 1.0 C B:CYS484 4.9 21.6 1.0 CB B:THR486 4.9 21.1 1.0 C B:MET483 4.9 23.3 1.0 O B:CYS465 4.9 15.6 1.0 HA B:CYS481 4.9 12.4 1.0 HA B:HIS467 5.0 12.8 1.0 N B:TYR485 5.0 18.6 1.0 CG B:MET483 5.0 30.8 1.0

M.Gabrielsen, L.Buetow, M.A.Nakasone, S.F.Ahmed, G.J.Sibbet, B.O.Smith, W.Zhang, S.S.Sidhu, D.T.Huang. A General Strategy For Discovery of Inhibitors and Activators of Ring and U-Box E3 Ligases with Ubiquitin Variants. Mol. Cell V. 68 456 2017.
ISSN: ISSN 1097-4164
PubMed: 29053960
DOI: 10.1016/J.MOLCEL.2017.09.027