Zinc in PDB 5cvo: WDR48:USP46~Ubiquitin Ternary Complex

All present enzymatic activity of WDR48:USP46~Ubiquitin Ternary Complex:
3.4.19.12;

The structure of WDR48:USP46~Ubiquitin Ternary Complex, PDB code: 5cvo was solved by S.F.Harris, J.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.70 / 3.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	211.342, 103.764, 190.954, 90.00, 119.03, 90.00
R / Rfree (%)	22.2 / 27.5

The binding sites of Zinc atom in the WDR48:USP46~Ubiquitin Ternary Complex (pdb code 5cvo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the WDR48:USP46~Ubiquitin Ternary Complex, PDB code: 5cvo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the WDR48:USP46~Ubiquitin Ternary Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of WDR48:USP46~Ubiquitin Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn900 b:82.4 occ:1.00 SG B:CYS185 2.2 0.2 1.0 SG B:CYS182 2.4 4.1 1.0 SG B:CYS229 2.4 3.6 1.0 SG B:CYS232 2.4 81.3 1.0 OG1 B:THR231 2.9 4.1 1.0 CB B:CYS182 3.2 4.7 1.0 CB B:CYS185 3.2 0.6 1.0 CB B:CYS229 3.4 4.2 1.0 N B:CYS185 3.5 4.7 1.0 CB B:CYS232 3.5 75.1 1.0 N B:CYS232 3.8 4.5 1.0 CA B:CYS185 3.9 4.2 1.0 OG1 B:THR187 4.1 25.6 1.0 CB B:THR231 4.2 4.0 1.0 CA B:CYS232 4.3 4.8 1.0 CB B:ASN184 4.4 13.5 1.0 C B:ASN184 4.5 25.9 1.0 CA B:CYS182 4.7 4.1 1.0 C B:THR231 4.7 12.6 1.0 C B:CYS185 4.7 5.6 1.0 N B:GLU186 4.8 5.8 1.0 CA B:ASN184 4.8 23.9 1.0 N B:ASN184 4.9 23.4 1.0 CA B:CYS229 4.9 21.3 1.0 CA B:THR231 4.9 12.1 1.0 N B:THR231 5.0 12.2 1.0

Zinc binding site 2 out of 2 in the WDR48:USP46~Ubiquitin Ternary Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of WDR48:USP46~Ubiquitin Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn900 b:80.8 occ:1.00 SG E:CYS185 2.2 0.2 1.0 SG E:CYS229 2.3 12.2 1.0 SG E:CYS232 2.3 49.4 1.0 SG E:CYS182 2.4 12.2 1.0 OG1 E:THR231 3.0 20.8 1.0 CB E:CYS182 3.2 12.1 1.0 CB E:CYS229 3.2 11.8 1.0 CB E:CYS185 3.3 0.8 1.0 CB E:CYS232 3.4 43.2 1.0 N E:CYS185 3.6 13.3 1.0 OG1 E:THR187 3.9 28.8 1.0 N E:CYS232 3.9 23.0 1.0 CA E:CYS185 4.0 14.2 1.0 CA E:CYS232 4.2 23.3 1.0 CB E:THR231 4.4 20.9 1.0 CB E:ASN184 4.4 12.8 1.0 CA E:CYS182 4.6 12.1 1.0 C E:ASN184 4.7 23.6 1.0 CA E:CYS229 4.7 31.1 1.0 C E:CYS185 4.8 13.6 1.0 C E:THR231 4.8 34.0 1.0 N E:ASN184 4.9 20.6 1.0 CA E:ASN184 4.9 21.3 1.0 N E:GLU186 4.9 13.2 1.0 C E:CYS182 5.0 13.1 1.0

J.Yin, A.J.Schoeffler, K.Wickliffe, K.Newton, M.A.Starovasnik, E.C.Dueber, S.F.Harris. Structural Insights Into Wd-Repeat 48 Activation of Ubiquitin-Specific Protease 46. Structure V. 23 2043 2015.
ISSN: ISSN 0969-2126
PubMed: 26388029
DOI: 10.1016/J.STR.2015.08.010