Zinc in PDB 6cpm: Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv

All present enzymatic activity of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv:
3.4.19.12;

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv, PDB code: 6cpm was solved by A.U.Singer, J.Teyra, G.Boehmelt, M.Lenter, F.Sicheri, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.21 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.552, 115.080, 95.701, 90.00, 92.59, 90.00
R / Rfree (%)	16.7 / 21.2

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv also contains other interesting chemical elements:

Calcium	(Ca)	5 atoms
Sodium	(Na)	3 atoms

The binding sites of Zinc atom in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv (pdb code 6cpm). 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 the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv, PDB code: 6cpm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn704 b:35.7 occ:1.00 SG C:CYS451 2.2 34.8 1.0 SG C:CYS448 2.3 33.1 1.0 SG C:CYS499 2.4 33.4 1.0 SG C:CYS502 2.4 37.2 1.0 CB C:CYS448 3.1 29.6 1.0 CB C:CYS451 3.2 36.8 1.0 CB C:CYS499 3.4 31.6 1.0 CB C:CYS502 3.5 36.3 1.0 N C:CYS451 3.7 36.6 1.0 N C:CYS502 3.7 37.3 1.0 CA C:CYS451 4.0 29.6 1.0 CA C:CYS502 4.2 36.2 1.0 CB C:ASN501 4.3 45.3 1.0 NE2 C:GLN506 4.4 41.0 1.0 CA C:CYS448 4.6 27.1 1.0 CG C:GLN506 4.7 40.6 1.0 C C:ASN501 4.7 41.1 1.0 O C:HOH989 4.7 41.5 1.0 C C:CYS451 4.7 28.7 1.0 CB C:GLU450 4.8 35.9 1.0 C C:GLU450 4.8 34.3 1.0 CA C:CYS499 4.8 33.5 1.0 N C:ALA452 4.9 32.2 1.0 CA C:ASN501 4.9 44.0 1.0 CB C:LYS453 5.0 43.4 1.0

Zinc binding site 2 out of 2 in the Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the USP15 Deubiquitinase Domain in Complex with A Third- Generation Inhibitory Ubv within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:35.7 occ:1.00 SG D:CYS451 2.3 32.4 1.0 SG D:CYS448 2.3 31.7 1.0 SG D:CYS502 2.4 37.5 1.0 SG D:CYS499 2.4 33.2 1.0 CB D:CYS448 3.1 27.8 1.0 CB D:CYS499 3.3 31.2 1.0 CB D:CYS451 3.3 35.8 1.0 CB D:CYS502 3.4 35.8 1.0 N D:CYS451 3.7 36.3 1.0 N D:CYS502 3.7 33.3 1.0 CA D:CYS451 4.1 33.6 1.0 CB D:ASN501 4.1 41.1 1.0 CA D:CYS502 4.2 39.1 1.0 NE2 D:GLN506 4.5 38.2 1.0 CA D:CYS448 4.6 27.1 1.0 CG D:GLN506 4.6 35.5 1.0 C D:ASN501 4.7 37.6 1.0 CA D:CYS499 4.7 33.2 1.0 CB D:GLU450 4.7 31.7 1.0 C D:GLU450 4.8 36.9 1.0 C D:CYS451 4.8 31.6 1.0 CA D:ASN501 4.9 41.9 1.0 OD1 D:ASN501 4.9 63.9 1.0 CB D:LYS453 4.9 44.9 1.0 N D:ALA452 5.0 31.6 1.0 N D:GLU450 5.0 31.3 1.0

J.Teyra, A.U.Singer, F.W.Schmitges, P.Jaynes, S.Kit Leng Lui, M.J.Polyak, N.Fodil, J.R.Krieger, J.Tong, C.Schwerdtfeger, B.B.Brasher, D.F.J.Ceccarelli, J.Moffat, F.Sicheri, M.F.Moran, P.Gros, P.J.A.Eichhorn, M.Lenter, G.Boehmelt, S.S.Sidhu. Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure V. 27 590 2019.
ISSN: ISSN 1878-4186
PubMed: 30713027
DOI: 10.1016/J.STR.2019.01.002