Zinc in PDB 5wch: Crystal Structure of the Catalytic Domain of Human USP9X

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human USP9X:
3.4.19.12;

The structure of Crystal Structure of the Catalytic Domain of Human USP9X, PDB code: 5wch was solved by A.Dong, Q.Zhang, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwards, Y.Tong, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.372, 79.048, 131.933, 90.00, 103.76, 90.00
R / Rfree (%)	20.7 / 26.1

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human USP9X (pdb code 5wch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Human USP9X, PDB code: 5wch:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human USP9X


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 the Catalytic Domain of Human USP9X within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2000 b:34.4 occ:1.00 ND1 A:HIS1729 2.2 37.8 1.0 SG A:CYS1771 2.3 31.8 1.0 SG A:CYS1774 2.3 40.9 1.0 SG A:CYS1727 2.4 30.1 1.0 CG A:HIS1729 3.2 37.9 1.0 CB A:CYS1774 3.2 39.7 1.0 CE1 A:HIS1729 3.2 39.2 1.0 CB A:CYS1727 3.3 31.1 1.0 CB A:CYS1771 3.4 36.0 1.0 CB A:HIS1729 3.4 37.1 1.0 N A:CYS1774 3.9 37.4 1.0 CA A:CYS1774 4.1 38.9 1.0 NE2 A:HIS1729 4.3 40.5 1.0 CD2 A:HIS1729 4.3 37.6 1.0 N A:HIS1729 4.3 34.7 1.0 CA A:HIS1729 4.5 36.3 1.0 CD A:PRO1728 4.5 34.3 1.0 OH A:TYR1731 4.6 33.8 1.0 CA A:CYS1727 4.7 30.9 1.0 CA A:CYS1771 4.8 37.0 1.0 C A:CYS1727 4.9 32.2 1.0 N A:PRO1728 4.9 34.8 1.0 CB A:LYS1773 4.9 40.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human USP9X


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 the Catalytic Domain of Human USP9X within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2000 b:31.2 occ:1.00 ND1 B:HIS1729 2.2 32.8 1.0 SG B:CYS1774 2.2 29.9 1.0 SG B:CYS1771 2.3 30.3 1.0 SG B:CYS1727 2.3 32.7 1.0 CB B:CYS1774 3.1 32.8 1.0 CE1 B:HIS1729 3.1 32.7 1.0 CG B:HIS1729 3.1 32.8 1.0 CB B:CYS1727 3.3 32.3 1.0 CB B:CYS1771 3.4 33.8 1.0 CB B:HIS1729 3.5 32.1 1.0 N B:CYS1774 3.8 29.7 1.0 CA B:CYS1774 4.1 31.6 1.0 NE2 B:HIS1729 4.2 34.5 1.0 CD2 B:HIS1729 4.2 32.7 1.0 N B:HIS1729 4.3 32.7 1.0 CD B:PRO1728 4.4 31.7 1.0 CA B:HIS1729 4.5 32.5 1.0 CA B:CYS1727 4.7 32.2 1.0 OH B:TYR1731 4.7 30.8 1.0 CB B:LYS1773 4.7 36.5 1.0 CA B:CYS1771 4.8 33.8 1.0 N B:PRO1728 4.8 32.0 1.0 C B:CYS1727 4.8 31.4 1.0 C B:LYS1773 4.9 31.1 1.0 CG2 B:VAL1778 5.0 40.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human USP9X


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Human USP9X within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2001 b:34.5 occ:1.00 ND1 C:HIS1729 2.1 39.2 1.0 SG C:CYS1727 2.3 31.9 1.0 SG C:CYS1774 2.3 42.6 1.0 SG C:CYS1771 2.3 34.6 1.0 CG C:HIS1729 3.0 39.1 1.0 CE1 C:HIS1729 3.0 39.5 1.0 CB C:CYS1774 3.2 40.7 1.0 CB C:HIS1729 3.4 37.4 1.0 CB C:CYS1771 3.4 36.5 1.0 CB C:CYS1727 3.4 33.2 1.0 N C:CYS1774 3.8 38.2 1.0 NE2 C:HIS1729 4.0 42.7 1.0 CD2 C:HIS1729 4.0 40.5 1.0 CA C:CYS1774 4.1 39.5 1.0 N C:HIS1729 4.3 35.4 1.0 CA C:HIS1729 4.4 35.8 1.0 CD C:PRO1728 4.6 37.0 1.0 OH C:TYR1731 4.6 36.3 1.0 CA C:CYS1727 4.8 34.1 1.0 CB C:LYS1773 4.8 46.2 1.0 CA C:CYS1771 4.8 37.5 1.0 C C:LYS1773 4.8 39.8 1.0 N C:PRO1728 4.9 35.5 1.0 C C:CYS1727 4.9 34.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human USP9X


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Human USP9X within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2000 b:29.8 occ:1.00 ND1 D:HIS1729 2.1 34.0 1.0 SG D:CYS1771 2.2 24.5 1.0 SG D:CYS1727 2.3 35.4 1.0 SG D:CYS1774 2.3 34.9 1.0 CE1 D:HIS1729 2.9 35.9 1.0 CB D:CYS1774 3.2 35.4 1.0 CG D:HIS1729 3.2 34.7 1.0 CB D:CYS1727 3.3 37.4 1.0 CB D:CYS1771 3.3 29.5 1.0 CB D:HIS1729 3.7 34.4 1.0 N D:CYS1774 3.8 33.2 1.0 NE2 D:HIS1729 4.1 39.0 1.0 CA D:CYS1774 4.1 33.9 1.0 CD2 D:HIS1729 4.3 36.4 1.0 N D:HIS1729 4.4 33.6 1.0 CD D:PRO1728 4.6 38.2 1.0 OH D:TYR1731 4.6 28.5 1.0 CA D:CYS1727 4.6 37.7 1.0 CA D:CYS1771 4.7 31.3 1.0 CA D:HIS1729 4.7 34.7 1.0 CB D:LYS1773 4.7 36.6 1.0 N D:PRO1728 4.8 37.6 1.0 C D:CYS1727 4.9 37.2 1.0 C D:LYS1773 4.9 33.9 1.0

P.Paudel, Q.Zhang, C.Leung, H.C.Greenberg, Y.Guo, Y.H.Chern, A.Dong, Y.Li, M.Vedadi, Z.Zhuang, Y.Tong. Crystal Structure and Activity-Based Labeling Reveal the Mechanisms For Linkage-Specific Substrate Recognition By Deubiquitinase USP9X. Proc. Natl. Acad. Sci. V. 116 7288 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30914461
DOI: 10.1073/PNAS.1815027116