Zinc in PDB 8itp: Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin

All present enzymatic activity of Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin:
3.4.19.12;

The structure of Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin, PDB code: 8itp was solved by E.E.Kim, S.C.Shin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.51 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.957, 93.399, 217.762, 90, 90, 90
R / Rfree (%)	24.6 / 28.4

The binding sites of Zinc atom in the Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin (pdb code 8itp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin, PDB code: 8itp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:63.9 occ:1.00 SG D:CYS218 2.3 60.2 1.0 SG D:CYS271 2.3 84.6 1.0 SG D:CYS221 2.3 77.4 1.0 CB D:CYS221 2.4 76.1 1.0 CB D:CYS218 2.9 58.5 1.0 CB D:CYS271 3.3 86.5 1.0 N D:CYS221 3.3 84.0 1.0 SG D:CYS274 3.4 85.2 1.0 CB D:CYS274 3.4 86.4 1.0 CA D:CYS221 3.5 79.9 1.0 N D:CYS274 3.8 89.7 1.0 CA D:CYS274 4.1 84.2 1.0 CA D:CYS218 4.3 50.0 1.0 C D:CYS221 4.5 80.1 1.0 C D:LYS220 4.6 68.9 1.0 C D:CYS218 4.6 52.6 1.0 CB D:ASN273 4.6 76.1 1.0 C D:ASN273 4.7 96.1 1.0 CA D:CYS271 4.7 78.1 1.0 O D:CYS218 4.7 55.0 1.0 N D:GLY222 4.7 63.6 1.0 N D:LYS220 5.0 65.7 1.0 CB D:LYS220 5.0 77.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of USP47 Catalytic Domain Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:62.6 occ:1.00 SG B:CYS218 2.3 88.8 1.0 SG B:CYS271 2.3 89.1 1.0 SG B:CYS221 2.3 76.8 1.0 SG B:CYS274 2.3 84.1 1.0 CB B:CYS221 3.0 77.0 1.0 CB B:CYS274 3.1 87.3 1.0 CB B:CYS271 3.1 89.5 1.0 CB B:CYS218 3.4 82.4 1.0 N B:CYS274 3.5 80.8 1.0 N B:CYS221 3.7 69.5 1.0 CA B:CYS274 3.7 75.4 1.0 CA B:CYS221 4.0 68.2 1.0 C B:ASN273 4.5 76.3 1.0 CA B:CYS271 4.5 70.0 1.0 C B:LYS220 4.7 73.1 1.0 CB B:LYS220 4.7 61.5 1.0 CB B:ASN273 4.8 112.2 1.0 CA B:CYS218 4.8 50.8 1.0 C B:CYS271 4.9 75.5 1.0

S.C.Shin, J.Park, K.H.Kim, J.M.Yoon, J.Cho, B.H.Ha, Y.Oh, H.Choo, E.J.Song, E.E.Kim. Structural and Functional Characterization of USP47 Reveals A Hot Spot For Inhibitor Design Commun Biol V. 6 970 2023.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-023-05345-5