Zinc in PDB 6ml1: Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv

All present enzymatic activity of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv:
3.4.19.12;

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv, PDB code: 6ml1 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)	49.32 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.770, 115.290, 95.320, 90.00, 91.92, 90.00
R / Rfree (%)	18.9 / 22

The structure of Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	4 atoms

The binding sites of Zinc atom in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured Inhibitory Ubv (pdb code 6ml1). 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 An Affinity-Matured Inhibitory Ubv, PDB code: 6ml1:
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 An Affinity-Matured 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 An Affinity-Matured Inhibitory Ubv within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:47.6 occ:1.00 SG A:CYS451 2.4 44.3 1.0 SG A:CYS448 2.4 42.0 1.0 SG A:CYS809 2.5 42.6 1.0 SG A:CYS812 2.5 52.1 1.0 CB A:CYS451 3.1 49.0 1.0 CB A:CYS448 3.1 45.3 1.0 CB A:CYS809 3.4 50.3 1.0 CB A:CYS812 3.4 58.7 1.0 N A:CYS451 3.7 42.1 1.0 N A:CYS812 3.8 56.0 1.0 CA A:CYS451 4.0 40.8 1.0 CA A:CYS812 4.2 61.2 1.0 CB A:ASN811 4.5 56.2 1.0 CA A:CYS448 4.6 41.2 1.0 C A:CYS451 4.7 44.6 1.0 CG A:GLN816 4.7 57.6 1.0 NE2 A:GLN816 4.8 54.0 1.0 C A:GLU450 4.8 46.7 1.0 C A:ASN811 4.8 62.6 1.0 CA A:CYS809 4.8 49.0 1.0 CB A:GLU450 4.8 48.5 1.0 CB A:LYS453 4.8 46.5 1.0 N A:ALA452 4.9 42.7 1.0 ND2 A:ASN811 5.0 66.0 1.0

Zinc binding site 2 out of 2 in the Structure of the USP15 Deubiquitinase Domain in Complex with An Affinity-Matured 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 An Affinity-Matured Inhibitory Ubv within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:40.0 occ:1.00 SG B:CYS448 2.3 37.3 1.0 SG B:CYS451 2.4 43.1 1.0 SG B:CYS812 2.4 41.3 1.0 SG B:CYS809 2.5 41.4 1.0 CB B:CYS448 3.1 34.0 1.0 CB B:CYS451 3.2 37.0 1.0 CB B:CYS809 3.3 42.6 1.0 CB B:CYS812 3.4 46.5 1.0 N B:CYS451 3.7 38.3 1.0 N B:CYS812 3.7 39.1 1.0 CA B:CYS451 4.0 38.8 1.0 CA B:CYS812 4.2 46.9 1.0 CB B:ASN811 4.4 47.4 1.0 NE2 B:GLN816 4.4 45.5 1.0 ND2 B:ASN811 4.5 57.4 1.0 CA B:CYS448 4.5 36.8 1.0 CB B:LYS453 4.6 37.7 1.0 C B:CYS451 4.7 37.8 1.0 CG B:GLN816 4.7 47.4 1.0 CB B:GLU450 4.7 48.8 1.0 CA B:CYS809 4.7 38.1 1.0 C B:ASN811 4.8 45.0 1.0 CG B:ASN811 4.9 61.7 1.0 C B:GLU450 4.9 45.4 1.0 CG B:GLU450 4.9 56.9 1.0 N B:ALA452 4.9 41.1 1.0 N B:LYS453 4.9 35.8 1.0 CD B:GLN816 5.0 57.3 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