Zinc in PDB 5gvi: Zebrafish USP30 in Complex with LYS6-Linked Diubiquitin

The structure of Zebrafish USP30 in Complex with LYS6-Linked Diubiquitin, PDB code: 5gvi was solved by Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.08 / 1.87
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	130.270, 130.270, 59.881, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 20.6

The binding sites of Zinc atom in the Zebrafish USP30 in Complex with LYS6-Linked Diubiquitin (pdb code 5gvi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Zebrafish USP30 in Complex with LYS6-Linked Diubiquitin, PDB code: 5gvi:

Zinc binding site 1 out of 1 in the Zebrafish USP30 in Complex with LYS6-Linked Diubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zebrafish USP30 in Complex with LYS6-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:67.1 occ:1.00 SG A:CYS283 2.3 75.4 1.0 SG A:CYS233 2.3 69.7 1.0 SG A:CYS280 2.3 64.6 1.0 SG A:CYS230 2.4 61.6 1.0 CB A:CYS230 3.1 55.5 1.0 CB A:CYS233 3.4 79.2 1.0 CB A:CYS280 3.4 62.6 1.0 CB A:CYS283 3.5 79.1 1.0 N A:CYS233 3.8 74.9 1.0 N A:CYS283 3.8 79.6 1.0 CA A:CYS233 4.2 77.1 1.0 CA A:CYS283 4.2 82.5 1.0 CB A:ASN282 4.4 82.0 1.0 OG1 A:THR302 4.4 63.0 1.0 CB A:ARG232 4.5 76.3 1.0 CA A:CYS230 4.5 59.7 1.0 CG2 A:THR302 4.6 65.3 1.0 C A:ARG232 4.7 75.6 1.0 CA A:CYS280 4.8 60.9 1.0 C A:ASN282 4.8 82.0 1.0 C A:CYS233 4.9 74.5 1.0 N A:ARG232 5.0 72.0 1.0 CA A:ARG232 5.0 72.7 1.0 C A:CYS230 5.0 62.6 1.0

Y.Sato, K.Okatsu, Y.Saeki, K.Yamano, N.Matsuda, A.Kaiho, A.Yamagata, S.Goto-Ito, M.Ishikawa, Y.Hashimoto, K.Tanaka, S.Fukai. Structural Basis For Specific Cleavage of LYS6-Linked Polyubiquitin Chains By USP30 Nat. Struct. Mol. Biol. V. 24 911 2017.
ISSN: ESSN 1545-9985
PubMed: 28945247
DOI: 10.1038/NSMB.3469