Zinc in PDB 6gh9: USP15 Catalytic Domain in Complex with Small Molecule

All present enzymatic activity of USP15 Catalytic Domain in Complex with Small Molecule:
3.4.19.12;

The structure of USP15 Catalytic Domain in Complex with Small Molecule, PDB code: 6gh9 was solved by S.J.Ward, H.E.Gratton, S.G.Caulton, J.Emsley, I.Dreveny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.07 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.070, 94.390, 63.290, 90.00, 90.08, 90.00
R / Rfree (%)	20.3 / 25.2

The binding sites of Zinc atom in the USP15 Catalytic Domain in Complex with Small Molecule (pdb code 6gh9). 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 USP15 Catalytic Domain in Complex with Small Molecule, PDB code: 6gh9:

Zinc binding site 1 out of 1 in the USP15 Catalytic Domain in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of USP15 Catalytic Domain in Complex with Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:92.3 occ:1.00 SG A:CYS422 2.3 93.2 1.0 SG A:CYS419 2.4 0.7 1.0 SG A:CYS783 2.5 0.1 1.0 SG A:CYS780 2.5 94.0 1.0 CB A:CYS780 3.3 93.4 1.0 CB A:CYS419 3.3 99.7 1.0 CB A:CYS422 3.5 98.1 1.0 N A:CYS422 3.6 0.8 1.0 CB A:CYS783 3.7 0.4 1.0 CB A:GLU421 3.9 0.7 1.0 OE1 A:GLU421 3.9 0.3 1.0 CA A:CYS422 4.2 0.8 1.0 C A:GLU421 4.4 0.2 1.0 N A:CYS783 4.4 0.5 1.0 CA A:GLU421 4.5 0.2 1.0 CA A:CYS783 4.6 0.1 1.0 N A:GLU421 4.7 0.8 1.0 CA A:CYS419 4.7 96.6 1.0 CB A:LYS424 4.7 89.1 1.0 CA A:CYS780 4.8 96.0 1.0 CD A:GLU421 4.8 0.4 1.0 CB A:ASN782 4.8 98.1 1.0 ND2 A:ASN782 4.9 0.1 1.0 O A:CYS419 4.9 97.2 1.0 C A:CYS422 4.9 0.3 1.0 C A:CYS419 5.0 91.3 1.0 CG A:GLU421 5.0 0.6 1.0

S.J.Ward, H.E.Gratton, P.Indrayudha, C.Michavila, R.Mukhopadhyay, S.K.Maurer, S.G.Caulton, J.Emsley, I.Dreveny. The Structure of the Deubiquitinase USP15 Reveals A Misaligned Catalytic Triad and An Open Ubiquitin-Binding Channel. J. Biol. Chem. V. 293 17362 2018.
ISSN: ESSN 1083-351X
PubMed: 30228188
DOI: 10.1074/JBC.RA118.003857