Zinc in PDB 2uzg: Zf-Ubp Domain of VDU1

The binding sites of Zinc atom in the Zf-Ubp Domain of VDU1 (pdb code 2uzg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Zf-Ubp Domain of VDU1, PDB code: 2uzg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Zf-Ubp Domain of VDU1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zf-Ubp Domain of VDU1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn131 b:0.0 occ:1.00 ND1 A:HIS41 2.0 0.0 1.0 SG A:CYS117 2.2 0.0 1.0 SG A:CYS114 2.3 0.0 1.0 SG A:CYS39 2.3 0.0 1.0 HB2 A:CYS117 2.7 0.0 1.0 CE1 A:HIS41 2.9 0.0 1.0 CB A:CYS117 3.0 0.0 1.0 H A:CYS117 3.0 0.0 1.0 HE1 A:HIS41 3.0 0.0 1.0 HB2 A:HIS41 3.0 0.0 1.0 HB2 A:CYS39 3.1 0.0 1.0 CG A:HIS41 3.2 0.0 1.0 CB A:CYS39 3.4 0.0 1.0 HB2 A:ALA116 3.4 0.0 1.0 N A:CYS117 3.6 0.0 1.0 CB A:HIS41 3.6 0.0 1.0 CB A:CYS114 3.7 0.0 1.0 HD2 A:PRO40 3.7 0.0 1.0 H A:HIS41 3.7 0.0 1.0 HB3 A:CYS114 3.7 0.0 1.0 CA A:CYS117 3.8 0.0 1.0 HB3 A:CYS117 3.9 0.0 1.0 HB2 A:CYS114 4.0 0.0 1.0 HB3 A:CYS39 4.1 0.0 1.0 HA A:CYS117 4.1 0.0 1.0 NE2 A:HIS41 4.1 0.0 1.0 H A:LEU42 4.2 0.0 1.0 HG12 A:VAL121 4.2 0.0 1.0 CD2 A:HIS41 4.2 0.0 1.0 HD22 A:LEU42 4.2 0.0 1.0 HB3 A:HIS41 4.4 0.0 1.0 CB A:ALA116 4.4 0.0 1.0 N A:HIS41 4.4 0.0 1.0 CA A:CYS39 4.5 0.0 1.0 HG2 A:PRO40 4.6 0.0 1.0 HA A:CYS39 4.6 0.0 1.0 C A:ALA116 4.6 0.0 1.0 HB1 A:ALA116 4.6 0.0 1.0 CA A:HIS41 4.7 0.0 1.0 CD A:PRO40 4.7 0.0 1.0 C A:CYS39 4.9 0.0 1.0 N A:PRO40 4.9 0.0 1.0 HE2 A:HIS41 4.9 0.0 1.0 H A:ALA116 5.0 0.0 1.0 CA A:ALA116 5.0 0.0 1.0 CA A:CYS114 5.0 0.0 1.0

Zinc binding site 2 out of 3 in the Zf-Ubp Domain of VDU1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zf-Ubp Domain of VDU1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn132 b:0.0 occ:1.00 ND1 A:HIS91 2.1 0.0 1.0 SG A:CYS61 2.4 0.0 1.0 SG A:CYS64 2.4 0.0 1.0 SG A:CYS84 2.4 0.0 1.0 CE1 A:HIS91 3.0 0.0 1.0 HE1 A:HIS91 3.1 0.0 1.0 H A:CYS84 3.1 0.0 1.0 HB2 A:HIS91 3.1 0.0 1.0 CG A:HIS91 3.2 0.0 1.0 H A:CYS64 3.3 0.0 1.0 CB A:CYS61 3.4 0.0 1.0 HB2 A:CYS61 3.4 0.0 1.0 HB3 A:CYS61 3.5 0.0 1.0 HG12 A:VAL66 3.6 0.0 1.0 CB A:HIS91 3.7 0.0 1.0 HB A:VAL89 3.7 0.0 1.0 HG23 A:VAL66 3.7 0.0 1.0 HB3 A:ASP63 3.8 0.0 1.0 CB A:CYS64 3.8 0.0 1.0 CB A:CYS84 3.8 0.0 1.0 N A:CYS84 3.9 0.0 1.0 HB3 A:CYS64 3.9 0.0 1.0 HB3 A:CYS84 3.9 0.0 1.0 HA2 A:GLY83 3.9 0.0 1.0 N A:CYS64 4.0 0.0 1.0 HB3 A:HIS91 4.0 0.0 1.0 HG22 A:VAL89 4.1 0.0 1.0 NE2 A:HIS91 4.2 0.0 1.0 HG22 A:VAL66 4.2 0.0 1.0 CD2 A:HIS91 4.3 0.0 1.0 HB2 A:ASP63 4.4 0.0 1.0 CA A:CYS64 4.4 0.0 1.0 CG2 A:VAL66 4.4 0.0 1.0 H A:ASP63 4.4 0.0 1.0 CA A:CYS84 4.4 0.0 1.0 HG21 A:VAL89 4.5 0.0 1.0 CB A:ASP63 4.5 0.0 1.0 CB A:VAL89 4.6 0.0 1.0 HB2 A:CYS64 4.6 0.0 1.0 H A:HIS91 4.6 0.0 1.0 HB2 A:CYS84 4.6 0.0 1.0 CG2 A:VAL89 4.6 0.0 1.0 CG1 A:VAL66 4.7 0.0 1.0 C A:GLY83 4.8 0.0 1.0 CA A:GLY83 4.8 0.0 1.0 CA A:CYS61 4.8 0.0 1.0 C A:CYS64 4.9 0.0 1.0 HB2 A:GLN88 4.9 0.0 1.0 C A:ASP63 5.0 0.0 1.0

Zinc binding site 3 out of 3 in the Zf-Ubp Domain of VDU1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zf-Ubp Domain of VDU1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn133 b:0.0 occ:1.00 NE2 A:HIS95 2.0 0.0 1.0 ND1 A:HIS101 2.0 0.0 1.0 SG A:CYS74 2.3 0.0 1.0 SG A:CYS79 2.4 0.0 1.0 HB3 A:CYS79 2.8 0.0 1.0 CE1 A:HIS101 2.8 0.0 1.0 HE1 A:HIS101 2.8 0.0 1.0 CE1 A:HIS95 2.9 0.0 1.0 CB A:CYS79 3.0 0.0 1.0 HE1 A:HIS95 3.1 0.0 1.0 HB2 A:CYS79 3.1 0.0 1.0 CD2 A:HIS95 3.2 0.0 1.0 HB2 A:CYS74 3.3 0.0 1.0 CG A:HIS101 3.3 0.0 1.0 CB A:CYS74 3.4 0.0 1.0 HD2 A:HIS95 3.5 0.0 1.0 HB2 A:HIS101 3.6 0.0 1.0 HB3 A:CYS74 3.6 0.0 1.0 OG1 A:THR99 3.7 0.0 1.0 HB2 A:TYR81 3.8 0.0 1.0 HB2 A:GLU76 3.8 0.0 1.0 CB A:HIS101 3.9 0.0 1.0 HB3 A:HIS101 3.9 0.0 1.0 HG1 A:THR99 4.0 0.0 1.0 HG23 A:THR99 4.0 0.0 1.0 NE2 A:HIS101 4.0 0.0 1.0 ND1 A:HIS95 4.1 0.0 1.0 HB3 A:GLU76 4.1 0.0 1.0 CG A:HIS95 4.3 0.0 1.0 CD2 A:HIS101 4.3 0.0 1.0 HB A:THR99 4.4 0.0 1.0 CA A:CYS79 4.4 0.0 1.0 CB A:GLU76 4.5 0.0 1.0 H A:TYR81 4.5 0.0 1.0 CB A:THR99 4.5 0.0 1.0 CG2 A:THR99 4.7 0.0 1.0 CB A:TYR81 4.8 0.0 1.0 CA A:CYS74 4.8 0.0 1.0 HB3 A:TYR81 4.8 0.0 1.0 HE2 A:HIS101 4.8 0.0 1.0 HA A:CYS79 4.8 0.0 1.0 H A:GLU76 4.9 0.0 1.0 HA A:CYS74 4.9 0.0 1.0 C A:CYS79 4.9 0.0 1.0 HD1 A:HIS95 5.0 0.0 1.0

M.D.Allen, M.Bycroft. The Solution Structure of the Znf Ubp Domain of USP33/VDU1. Protein Sci. V. 16 2072 2007.
ISSN: ISSN 0961-8368
PubMed: 17766394
DOI: 10.1110/PS.072967807