Zinc in PDB 6kcz: Solution Structure of the Znf-Ubp Domain of USP20/VDU2

All present enzymatic activity of Solution Structure of the Znf-Ubp Domain of USP20/VDU2:
3.4.19.12;

The binding sites of Zinc atom in the Solution Structure of the Znf-Ubp Domain of USP20/VDU2 (pdb code 6kcz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Solution Structure of the Znf-Ubp Domain of USP20/VDU2, PDB code: 6kcz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Solution Structure of the Znf-Ubp Domain of USP20/VDU2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of the Znf-Ubp Domain of USP20/VDU2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:0.0 occ:1.00 ND1 A:HIS10 2.0 0.0 1.0 SG A:CYS83 2.3 0.0 1.0 SG A:CYS86 2.3 0.0 1.0 SG A:CYS8 2.3 0.0 1.0 HG2 A:PRO9 2.5 0.0 1.0 H A:HIS10 2.7 0.0 1.0 CE1 A:HIS10 2.9 0.0 1.0 HD2 A:PRO9 2.9 0.0 1.0 HE1 A:HIS10 3.0 0.0 1.0 H A:CYS86 3.0 0.0 1.0 CG A:HIS10 3.2 0.0 1.0 HB2 A:HIS10 3.2 0.0 1.0 CG A:PRO9 3.3 0.0 1.0 HB2 A:ALA85 3.4 0.0 1.0 CB A:CYS83 3.4 0.0 1.0 HB2 A:CYS8 3.4 0.0 1.0 HB2 A:CYS86 3.5 0.0 1.0 CD A:PRO9 3.5 0.0 1.0 N A:HIS10 3.5 0.0 1.0 HD21 A:LEU72 3.6 0.0 1.0 HB2 A:CYS83 3.6 0.0 1.0 HB3 A:CYS83 3.6 0.0 1.0 CB A:CYS86 3.6 0.0 1.0 CB A:CYS8 3.6 0.0 1.0 CB A:HIS10 3.7 0.0 1.0 OD1 A:ASN71 3.8 0.0 1.0 N A:CYS86 3.8 0.0 1.0 HG3 A:PRO9 3.8 0.0 1.0 HG A:LEU72 4.0 0.0 1.0 N A:PRO9 4.0 0.0 1.0 HD13 A:LEU72 4.0 0.0 1.0 NE2 A:HIS10 4.1 0.0 1.0 H A:LEU11 4.1 0.0 1.0 CA A:HIS10 4.2 0.0 1.0 HB1 A:ALA85 4.2 0.0 1.0 CD2 A:HIS10 4.2 0.0 1.0 CB A:ALA85 4.3 0.0 1.0 HB3 A:CYS8 4.3 0.0 1.0 CA A:CYS86 4.3 0.0 1.0 HB3 A:CYS86 4.4 0.0 1.0 CD2 A:LEU72 4.4 0.0 1.0 CB A:PRO9 4.5 0.0 1.0 HD3 A:PRO9 4.5 0.0 1.0 C A:CYS8 4.5 0.0 1.0 C A:PRO9 4.5 0.0 1.0 CA A:CYS8 4.6 0.0 1.0 CG A:LEU72 4.6 0.0 1.0 HB2 A:ASN71 4.6 0.0 1.0 CA A:PRO9 4.6 0.0 1.0 HB2 A:PRO9 4.6 0.0 1.0 HB3 A:HIS10 4.6 0.0 1.0 N A:LEU11 4.7 0.0 1.0 HD22 A:LEU72 4.7 0.0 1.0 CD1 A:LEU72 4.7 0.0 1.0 HA A:CYS8 4.8 0.0 1.0 CG A:ASN71 4.8 0.0 1.0 H A:ALA85 4.8 0.0 1.0 CA A:CYS83 4.8 0.0 1.0 C A:HIS10 4.8 0.0 1.0 HA A:CYS86 4.9 0.0 1.0 HA A:CYS83 4.9 0.0 1.0 C A:ALA85 4.9 0.0 1.0 HD12 A:LEU72 4.9 0.0 1.0 HE2 A:HIS10 5.0 0.0 1.0

Zinc binding site 2 out of 3 in the Solution Structure of the Znf-Ubp Domain of USP20/VDU2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of the Znf-Ubp Domain of USP20/VDU2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:0.0 occ:1.00 ND1 A:HIS60 2.0 0.0 1.0 SG A:CYS33 2.3 0.0 1.0 SG A:CYS53 2.3 0.0 1.0 SG A:CYS30 2.3 0.0 1.0 H A:CYS53 2.8 0.0 1.0 CE1 A:HIS60 2.9 0.0 1.0 HE1 A:HIS60 3.0 0.0 1.0 HB2 A:CYS33 3.0 0.0 1.0 HB2 A:HIS60 3.1 0.0 1.0 CG A:HIS60 3.2 0.0 1.0 CB A:CYS33 3.3 0.0 1.0 N A:CYS53 3.4 0.0 1.0 HA2 A:GLY52 3.4 0.0 1.0 HB2 A:SER32 3.5 0.0 1.0 HD2 A:PHE57 3.5 0.0 1.0 CB A:CYS30 3.6 0.0 1.0 CB A:CYS53 3.6 0.0 1.0 HB2 A:CYS30 3.7 0.0 1.0 CB A:HIS60 3.7 0.0 1.0 H A:CYS33 3.7 0.0 1.0 H A:HIS60 3.7 0.0 1.0 HB3 A:CYS53 3.7 0.0 1.0 HB3 A:CYS30 3.8 0.0 1.0 N A:CYS33 3.9 0.0 1.0 H A:SER32 4.0 0.0 1.0 HB3 A:CYS33 4.1 0.0 1.0 NE2 A:HIS60 4.1 0.0 1.0 C A:GLY52 4.1 0.0 1.0 CA A:CYS53 4.1 0.0 1.0 CA A:GLY52 4.1 0.0 1.0 CD2 A:HIS60 4.2 0.0 1.0 CA A:CYS33 4.2 0.0 1.0 HB1 A:ALA58 4.3 0.0 1.0 HA3 A:GLY52 4.3 0.0 1.0 C A:SER32 4.4 0.0 1.0 CB A:SER32 4.4 0.0 1.0 CD2 A:PHE57 4.4 0.0 1.0 N A:HIS60 4.4 0.0 1.0 HG11 A:VAL35 4.4 0.0 1.0 HE2 A:PHE57 4.5 0.0 1.0 HB3 A:HIS60 4.5 0.0 1.0 HB2 A:CYS53 4.5 0.0 1.0 CA A:HIS60 4.6 0.0 1.0 HB3 A:SER32 4.6 0.0 1.0 HA A:CYS53 4.7 0.0 1.0 N A:SER32 4.7 0.0 1.0 CA A:SER32 4.8 0.0 1.0 H A:ALA58 4.8 0.0 1.0 HB3 A:PHE57 4.8 0.0 1.0 HA A:CYS33 4.8 0.0 1.0 HA A:HIS60 4.8 0.0 1.0 CE2 A:PHE57 4.9 0.0 1.0 CA A:CYS30 4.9 0.0 1.0 HE2 A:HIS60 4.9 0.0 1.0

Zinc binding site 3 out of 3 in the Solution Structure of the Znf-Ubp Domain of USP20/VDU2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Solution Structure of the Znf-Ubp Domain of USP20/VDU2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:0.0 occ:1.00 ND1 A:HIS70 2.0 0.0 1.0 NE2 A:HIS64 2.0 0.0 1.0 SG A:CYS48 2.3 0.0 1.0 SG A:CYS43 2.3 0.0 1.0 CE1 A:HIS70 3.0 0.0 1.0 CG A:HIS70 3.0 0.0 1.0 CE1 A:HIS64 3.0 0.0 1.0 CD2 A:HIS64 3.0 0.0 1.0 HG3 A:GLN45 3.0 0.0 1.0 HB2 A:HIS70 3.1 0.0 1.0 HB2 A:CYS43 3.1 0.0 1.0 CB A:CYS43 3.2 0.0 1.0 HE1 A:HIS70 3.2 0.0 1.0 HB3 A:CYS48 3.3 0.0 1.0 HE1 A:HIS64 3.3 0.0 1.0 CB A:CYS48 3.3 0.0 1.0 HD2 A:HIS64 3.3 0.0 1.0 HB3 A:CYS43 3.3 0.0 1.0 CB A:HIS70 3.4 0.0 1.0 HB3 A:HIS70 3.4 0.0 1.0 HB2 A:CYS48 3.5 0.0 1.0 HB2 A:LYS68 3.7 0.0 1.0 HD3 A:LYS68 4.0 0.0 1.0 CG A:GLN45 4.0 0.0 1.0 NE2 A:HIS70 4.1 0.0 1.0 CD2 A:HIS70 4.1 0.0 1.0 HG2 A:GLN45 4.1 0.0 1.0 ND1 A:HIS64 4.2 0.0 1.0 HB3 A:LYS68 4.2 0.0 1.0 CG A:HIS64 4.2 0.0 1.0 HG2 A:LYS68 4.4 0.0 1.0 CB A:LYS68 4.4 0.0 1.0 HD1 A:TYR50 4.5 0.0 1.0 CA A:CYS43 4.6 0.0 1.0 CA A:CYS48 4.6 0.0 1.0 HB2 A:GLN45 4.7 0.0 1.0 H A:GLN45 4.7 0.0 1.0 CG A:LYS68 4.8 0.0 1.0 O A:CYS48 4.8 0.0 1.0 HA A:CYS43 4.8 0.0 1.0 CD A:LYS68 4.8 0.0 1.0 CD A:GLN45 4.8 0.0 1.0 CA A:HIS70 4.9 0.0 1.0 HA A:CYS48 4.9 0.0 1.0 H A:HIS70 5.0 0.0 1.0 HE2 A:HIS70 5.0 0.0 1.0

Y.Yang, Y.Ding, C.Zhou, Y.Wen, N.Zhang. Structural and Functional Studies of USP20 Znf-Ubp Domain By uc(Nmr). Protein Sci. V. 28 1606 2019.
ISSN: ESSN 1469-896X
PubMed: 31278784
DOI: 10.1002/PRO.3675