Zinc in PDB 6dxt: Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate

All present enzymatic activity of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate:
3.4.19.12;

The structure of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate, PDB code: 6dxt was solved by M.K.Mann, R.J.Harding, M.Ravichandran, R.Ferreira De Freitas, I.Franzoni, C.Bountra, A.M.Edwards, C.M.Arrowsmith, M.Schapira, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.07 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.090, 85.440, 59.740, 90.00, 100.29, 90.00
R / Rfree (%)	19.4 / 24.2

The binding sites of Zinc atom in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate (pdb code 6dxt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate, PDB code: 6dxt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:22.3 occ:1.00 ND1 A:HIS232 2.1 22.0 1.0 SG A:CYS199 2.3 19.9 1.0 SG A:CYS219 2.3 20.6 1.0 SG A:CYS202 2.4 23.5 1.0 CE1 A:HIS232 3.0 25.4 1.0 CG A:HIS232 3.1 22.2 1.0 CB A:CYS199 3.2 20.1 1.0 CB A:CYS219 3.4 17.1 1.0 CB A:HIS232 3.4 20.9 1.0 CB A:CYS202 3.4 24.3 1.0 N A:CYS202 3.9 23.1 1.0 N A:CYS219 4.0 16.9 1.0 CA A:CYS202 4.2 24.0 1.0 NE2 A:HIS232 4.2 25.4 1.0 CD2 A:HIS232 4.2 24.2 1.0 CB A:ASN230 4.3 23.6 1.0 C A:LYS201 4.3 25.2 1.0 CB A:LYS201 4.3 27.4 1.0 CA A:CYS219 4.3 18.5 1.0 CG A:MET204 4.3 36.3 1.0 CA A:CYS199 4.6 20.4 1.0 ND2 A:ASN230 4.7 26.8 1.0 CA A:LYS201 4.7 25.9 1.0 CA A:HIS232 4.7 19.8 1.0 N A:HIS232 4.7 19.5 1.0 N A:LYS201 4.7 22.7 1.0 O A:LYS201 4.7 28.1 1.0 CB A:MET204 4.8 30.6 1.0 C A:CYS202 4.8 24.4 1.0 N A:ASN230 4.9 21.7 1.0 CA A:ASN230 5.0 23.1 1.0 CG A:ASN230 5.0 29.6 1.0

Zinc binding site 2 out of 2 in the Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:19.2 occ:1.00 ND1 B:HIS232 2.1 18.7 1.0 SG B:CYS219 2.3 15.7 1.0 SG B:CYS202 2.3 19.4 1.0 SG B:CYS199 2.4 16.7 1.0 CE1 B:HIS232 3.0 20.2 1.0 CG B:HIS232 3.1 18.8 1.0 CB B:CYS199 3.3 17.9 1.0 CB B:CYS219 3.4 16.0 1.0 CB B:HIS232 3.4 17.4 1.0 CB B:CYS202 3.5 21.6 1.0 N B:CYS202 3.8 21.4 1.0 N B:CYS219 4.0 14.2 1.0 CA B:CYS202 4.2 23.2 1.0 NE2 B:HIS232 4.2 19.5 1.0 CD2 B:HIS232 4.2 19.5 1.0 CB B:ASN230 4.2 20.9 1.0 CA B:CYS219 4.3 15.2 1.0 C B:LYS201 4.4 22.8 1.0 CG B:MET204 4.4 33.7 1.0 CB B:LYS201 4.4 23.7 1.0 ND2 B:ASN230 4.6 23.7 1.0 CB B:MET204 4.6 28.5 1.0 N B:HIS232 4.7 16.1 1.0 CA B:HIS232 4.7 16.5 1.0 CA B:CYS199 4.7 16.9 1.0 CA B:LYS201 4.7 22.9 1.0 N B:LYS201 4.8 20.8 1.0 C B:CYS202 4.8 25.4 1.0 CG B:ASN230 4.9 23.0 1.0 N B:ASN230 5.0 19.3 1.0 CA B:ASN230 5.0 20.9 1.0 O B:LYS201 5.0 23.1 1.0

M.K.Mann, R.J.Harding, M.Ravichandran, R.Ferreira De Freitas, I.Franzoni, C.Bountra, A.M.Edwards, C.M.Arrowsmith, M.Schapira, Structural Genomics Consortium (Sgc). Structure of USP5 Zinc-Finger Ubiquitin Binding Domain Co-Crystallized with 3-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Propanoate To Be Published.