Zinc in PDB 7w3u: USP34 Catalytic Domain in Complex with Ubpa

All present enzymatic activity of USP34 Catalytic Domain in Complex with Ubpa:
3.4.19.12;

The structure of USP34 Catalytic Domain in Complex with Ubpa, PDB code: 7w3u was solved by G.L.Xu, Z.H.Ming, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.60 / 3.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	192.02, 71.33, 111.69, 90, 90, 90
R / Rfree (%)	21.7 / 24.5

The binding sites of Zinc atom in the USP34 Catalytic Domain in Complex with Ubpa (pdb code 7w3u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the USP34 Catalytic Domain in Complex with Ubpa, PDB code: 7w3u:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the USP34 Catalytic Domain in Complex with Ubpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of USP34 Catalytic Domain in Complex with Ubpa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2301 b:116.1 occ:1.00 SG A:CYS2062 2.3 106.7 1.0 SG A:CYS2018 2.5 136.2 1.0 SG A:CYS2065 2.5 111.2 1.0 ND1 A:HIS2020 2.6 108.4 1.0 CE1 A:HIS2020 3.1 110.2 1.0 CB A:CYS2065 3.1 112.4 1.0 CB A:CYS2062 3.2 107.3 1.0 CB A:CYS2018 3.3 132.7 1.0 CG A:HIS2020 3.4 106.9 1.0 NE2 A:HIS2020 3.9 109.0 1.0 CB A:HIS2020 4.0 105.6 1.0 CD2 A:HIS2020 4.1 108.4 1.0 CA A:CYS2065 4.4 116.1 1.0 N A:CYS2065 4.5 117.9 1.0 CA A:CYS2018 4.6 130.1 1.0 OE1 A:GLU2019 4.6 138.3 1.0 C A:HIS2064 4.7 119.7 1.0 CA A:CYS2062 4.7 107.9 1.0 CG1 A:VAL2069 4.8 97.1 1.0 O A:HIS2064 4.8 121.4 1.0 N A:GLU2019 4.9 126.8 1.0

Zinc binding site 2 out of 3 in the USP34 Catalytic Domain in Complex with Ubpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of USP34 Catalytic Domain in Complex with Ubpa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2301 b:118.0 occ:1.00 NE2 B:HIS2020 2.0 121.9 1.0 SG B:CYS2018 2.3 117.9 1.0 SG B:CYS2065 2.4 113.8 1.0 SG B:CYS2062 2.6 107.0 1.0 CB B:CYS2065 2.6 115.4 1.0 CB B:CYS2018 2.9 122.2 1.0 CE1 B:HIS2020 2.9 124.1 1.0 CD2 B:HIS2020 3.0 121.1 1.0 N B:CYS2065 3.6 113.6 1.0 CA B:CYS2065 3.7 119.4 1.0 CB B:CYS2062 3.7 107.3 1.0 ND1 B:HIS2020 4.0 122.5 1.0 CG B:HIS2020 4.0 121.0 1.0 CG2 B:VAL2069 4.3 112.5 1.0 CA B:CYS2018 4.4 124.9 1.0 CG1 B:VAL2069 4.6 108.0 1.0 C B:HIS2064 4.7 110.6 1.0 CB B:HIS2064 4.8 105.7 1.0 N B:CYS2018 4.8 128.9 1.0 C B:CYS2065 4.9 126.3 1.0 CB B:VAL2069 5.0 109.8 1.0 O B:CYS2062 5.0 106.0 1.0

Zinc binding site 3 out of 3 in the USP34 Catalytic Domain in Complex with Ubpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of USP34 Catalytic Domain in Complex with Ubpa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2301 b:147.1 occ:1.00 CD2 C:HIS2020 2.2 153.5 1.0 SG C:CYS2062 2.3 157.7 1.0 SG C:CYS2065 2.4 159.4 1.0 CG C:HIS2020 2.5 151.8 1.0 SG C:CYS2018 2.6 160.1 1.0 NE2 C:HIS2020 2.6 155.8 1.0 ND1 C:HIS2020 3.1 151.9 1.0 CB C:CYS2018 3.1 162.2 1.0 CE1 C:HIS2020 3.1 155.6 1.0 CB C:HIS2020 3.3 148.1 1.0 CB C:CYS2065 3.5 158.6 1.0 CB C:CYS2062 3.8 156.0 1.0 N C:CYS2065 4.2 157.8 1.0 CA C:CYS2018 4.3 160.4 1.0 N C:HIS2020 4.3 151.8 1.0 C C:CYS2018 4.4 157.2 1.0 CA C:HIS2020 4.4 148.5 1.0 CA C:CYS2065 4.5 159.9 1.0 N C:GLU2019 4.5 158.4 1.0 O C:CYS2018 4.8 154.9 1.0 C C:GLU2019 4.9 157.5 1.0

G.Xu, H.Su, L.Lu, X.Liu, L.Zhao, B.Tang, Z.Ming. Structural Insights Into the Catalytic Mechanism and Ubiquitin Recognition of USP34. J.Mol.Biol. V. 434 67634 2022.
ISSN: ESSN 1089-8638
PubMed: 35588869
DOI: 10.1016/J.JMB.2022.167634