Zinc in PDB 5vsk: Structure of Dub Complex

All present enzymatic activity of Structure of Dub Complex:
3.4.19.12;

The structure of Structure of Dub Complex, PDB code: 5vsk was solved by H.-Y.Seo, S.Dhe-Paganon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.15 / 3.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.390, 69.630, 77.970, 90.00, 99.16, 90.00
R / Rfree (%)	21.8 / 27.4

The structure of Structure of Dub Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Structure of Dub Complex (pdb code 5vsk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Dub Complex, PDB code: 5vsk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Dub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Dub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:0.4 occ:1.00 SG A:CYS300 2.3 91.2 1.0 OD2 A:ASP349 2.4 0.6 1.0 ND1 A:HIS403 2.4 78.7 1.0 OD1 A:ASP349 2.5 0.3 1.0 CG A:ASP349 2.8 0.8 1.0 CB A:CYS300 3.0 96.1 1.0 CE1 A:HIS403 3.3 77.4 1.0 CG A:HIS403 3.4 76.8 1.0 CB A:HIS403 3.7 74.8 1.0 NE2 A:GLN405 4.1 0.0 1.0 CE A:MET515 4.2 71.7 1.0 CB A:ASP349 4.3 0.2 1.0 NE2 A:HIS403 4.4 76.1 1.0 CA A:CYS300 4.4 88.0 1.0 CD2 A:HIS403 4.5 76.3 1.0 O A:TYR348 4.7 0.9 1.0 C A:CYS300 4.8 94.4 1.0 CA A:GLN297 4.9 91.1 1.0

Zinc binding site 2 out of 4 in the Structure of Dub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Dub Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:0.8 occ:1.00 OD2 A:ASP481 1.7 0.5 1.0 CE1 A:HIS464 2.1 0.5 1.0 CG A:ASP481 2.3 0.8 1.0 OD1 A:ASP481 2.3 0.7 1.0 NE2 A:HIS464 2.8 0.6 1.0 ND1 A:HIS464 3.0 0.6 1.0 CB A:ASP481 3.8 0.5 1.0 CD2 A:HIS464 3.9 0.8 1.0 CG A:HIS464 3.9 0.9 1.0 O A:ASP481 4.1 0.8 1.0 C A:ASP481 4.5 0.7 1.0 CA A:ASP481 4.5 0.2 1.0

Zinc binding site 3 out of 4 in the Structure of Dub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Dub Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:92.3 occ:1.00 ND1 B:HIS403 2.1 0.1 1.0 SG B:CYS300 2.4 93.9 1.0 CG B:HIS403 3.1 0.1 1.0 CE1 B:HIS403 3.1 0.2 1.0 CB B:CYS300 3.2 77.2 1.0 CB B:HIS403 3.3 91.0 1.0 OD2 B:ASP349 3.7 0.4 1.0 CB B:ASP349 4.0 0.2 1.0 NE2 B:GLN405 4.1 0.1 1.0 CE B:MET515 4.2 92.2 1.0 CD2 B:HIS403 4.2 0.5 1.0 NE2 B:HIS403 4.2 0.2 1.0 CG B:ASP349 4.3 0.8 1.0 O B:TYR348 4.4 0.8 1.0 CA B:CYS300 4.6 74.9 1.0 CA B:HIS403 4.9 0.7 1.0 CA B:ASP349 4.9 0.1 1.0 CA B:GLN297 5.0 80.6 1.0 C B:CYS300 5.0 90.2 1.0

Zinc binding site 4 out of 4 in the Structure of Dub Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Dub Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:0.7 occ:1.00 OD1 B:ASP481 2.6 1.0 1.0 OD2 B:ASP481 3.1 0.7 1.0 CG B:ASP481 3.2 0.9 1.0 CB B:HIS464 3.5 0.4 1.0 CG B:HIS464 4.0 0.9 1.0 ND1 B:HIS464 4.0 0.9 1.0 CA B:HIS464 4.2 0.7 1.0 CB B:ASP481 4.7 0.9 1.0 OD2 B:ASP482 4.9 0.5 1.0 CD2 B:HIS464 4.9 0.9 1.0 CE1 B:HIS464 5.0 0.1 1.0

I.Lamberto, X.Liu, H.S.Seo, N.J.Schauer, R.E.Iacob, W.Hu, D.Das, T.Mikhailova, E.L.Weisberg, J.R.Engen, K.C.Anderson, D.Chauhan, S.Dhe-Paganon, S.J.Buhrlage. Structure-Guided Development of A Potent and Selective Non-Covalent Active-Site Inhibitor of USP7. Cell Chem Biol V. 24 1490 2017.
ISSN: ESSN 2451-9456
PubMed: 29056421
DOI: 10.1016/J.CHEMBIOL.2017.09.003