Zinc in PDB 2i50: Solution Structure of Ubp-M Znf-Ubp Domain

All present enzymatic activity of Solution Structure of Ubp-M Znf-Ubp Domain:
3.1.2.15;

The binding sites of Zinc atom in the Solution Structure of Ubp-M Znf-Ubp Domain (pdb code 2i50). 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 Ubp-M Znf-Ubp Domain, PDB code: 2i50:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Solution Structure of Ubp-M Znf-Ubp Domain


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 Ubp-M Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn336 b:0.0 occ:1.00 ND1 A:HIS73 2.0 0.0 1.0 SG A:CYS31 2.3 0.0 1.0 SG A:CYS34 2.3 0.0 1.0 SG A:CYS65 2.3 0.0 1.0 HB2 A:HIS73 2.7 0.0 1.0 CE1 A:HIS73 3.0 0.0 1.0 HB3 A:CYS31 3.0 0.0 1.0 CG A:HIS73 3.1 0.0 1.0 HE1 A:HIS73 3.1 0.0 1.0 H A:CYS65 3.1 0.0 1.0 HB3 A:CYS65 3.2 0.0 1.0 CB A:CYS31 3.3 0.0 1.0 CB A:HIS73 3.4 0.0 1.0 CB A:CYS34 3.4 0.0 1.0 CB A:CYS65 3.4 0.0 1.0 H A:CYS34 3.5 0.0 1.0 HA A:CYS34 3.6 0.0 1.0 HB2 A:CYS34 3.6 0.0 1.0 N A:CYS34 3.6 0.0 1.0 HB2 A:CYS31 3.7 0.0 1.0 CA A:CYS34 3.7 0.0 1.0 HB3 A:ASP33 3.8 0.0 1.0 N A:CYS65 3.8 0.0 1.0 H A:HIS73 3.8 0.0 1.0 HB3 A:HIS73 3.9 0.0 1.0 HB2 A:GLU71 4.0 0.0 1.0 HA2 A:GLY64 4.0 0.0 1.0 NE2 A:HIS73 4.2 0.0 1.0 CD2 A:HIS73 4.2 0.0 1.0 HB2 A:CYS65 4.2 0.0 1.0 CA A:CYS65 4.3 0.0 1.0 C A:ASP33 4.3 0.0 1.0 HB3 A:CYS34 4.4 0.0 1.0 O A:CYS31 4.5 0.0 1.0 N A:HIS73 4.6 0.0 1.0 CA A:CYS31 4.6 0.0 1.0 CA A:HIS73 4.7 0.0 1.0 C A:GLY64 4.8 0.0 1.0 CB A:ASP33 4.8 0.0 1.0 C A:CYS31 4.8 0.0 1.0 HB3 A:GLU71 4.8 0.0 1.0 CA A:GLY64 4.8 0.0 1.0 O A:ASP33 4.8 0.0 1.0 H A:ASP33 4.8 0.0 1.0 HG3 A:GLU71 4.9 0.0 1.0 CB A:GLU71 4.9 0.0 1.0 CA A:ASP33 4.9 0.0 1.0

Zinc binding site 2 out of 3 in the Solution Structure of Ubp-M Znf-Ubp Domain


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 Ubp-M Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn337 b:0.0 occ:1.00 ND1 A:HIS86 2.1 0.0 1.0 NE2 A:HIS77 2.1 0.0 1.0 SG A:CYS60 2.3 0.0 1.0 SG A:CYS57 2.3 0.0 1.0 HB3 A:HIS86 2.7 0.0 1.0 CE1 A:HIS86 3.1 0.0 1.0 CG A:HIS86 3.1 0.0 1.0 CE1 A:HIS77 3.1 0.0 1.0 CD2 A:HIS77 3.2 0.0 1.0 HB3 A:CYS60 3.2 0.0 1.0 HB3 A:HIS62 3.3 0.0 1.0 HE1 A:HIS86 3.3 0.0 1.0 HE1 A:HIS77 3.3 0.0 1.0 HD2 A:HIS77 3.4 0.0 1.0 CB A:CYS60 3.4 0.0 1.0 CB A:HIS86 3.4 0.0 1.0 CB A:CYS57 3.4 0.0 1.0 HB3 A:CYS57 3.4 0.0 1.0 HB3 A:LYS59 3.5 0.0 1.0 H A:CYS60 3.6 0.0 1.0 HB2 A:CYS57 3.6 0.0 1.0 HB2 A:HIS62 3.9 0.0 1.0 N A:CYS60 4.0 0.0 1.0 H A:HIS62 4.0 0.0 1.0 HB2 A:HIS86 4.1 0.0 1.0 CB A:HIS62 4.1 0.0 1.0 HB2 A:CYS60 4.2 0.0 1.0 NE2 A:HIS86 4.2 0.0 1.0 CD2 A:HIS86 4.2 0.0 1.0 CA A:CYS60 4.2 0.0 1.0 ND1 A:HIS77 4.3 0.0 1.0 HG3 A:LYS59 4.3 0.0 1.0 CG A:HIS77 4.3 0.0 1.0 HG2 A:LYS59 4.4 0.0 1.0 HA A:HIS86 4.4 0.0 1.0 CB A:LYS59 4.5 0.0 1.0 CA A:HIS86 4.5 0.0 1.0 CG A:LYS59 4.7 0.0 1.0 C A:LYS59 4.8 0.0 1.0 O A:HIS86 4.8 0.0 1.0 CA A:CYS57 4.9 0.0 1.0 N A:HIS62 4.9 0.0 1.0 H A:GLY61 4.9 0.0 1.0 CG A:HIS62 4.9 0.0 1.0 C A:CYS60 5.0 0.0 1.0 H A:LYS59 5.0 0.0 1.0

Zinc binding site 3 out of 3 in the Solution Structure of Ubp-M Znf-Ubp Domain


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 Ubp-M Znf-Ubp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn338 b:0.0 occ:1.00 ND1 A:HIS9 2.1 0.0 1.0 SG A:CYS102 2.3 0.0 1.0 SG A:CYS7 2.3 0.0 1.0 SG A:CYS99 2.3 0.0 1.0 HB2 A:HIS9 2.6 0.0 1.0 CE1 A:HIS9 3.1 0.0 1.0 CG A:HIS9 3.1 0.0 1.0 HG11 A:VAL101 3.2 0.0 1.0 HB2 A:CYS102 3.2 0.0 1.0 HE1 A:HIS9 3.3 0.0 1.0 HB2 A:CYS7 3.4 0.0 1.0 CB A:CYS102 3.4 0.0 1.0 CB A:HIS9 3.4 0.0 1.0 HB3 A:CYS99 3.5 0.0 1.0 CB A:CYS99 3.5 0.0 1.0 CB A:CYS7 3.5 0.0 1.0 H A:HIS9 3.6 0.0 1.0 HB2 A:CYS99 3.7 0.0 1.0 H A:CYS102 3.8 0.0 1.0 HG12 A:VAL101 4.0 0.0 1.0 CG1 A:VAL101 4.0 0.0 1.0 N A:CYS102 4.0 0.0 1.0 HB3 A:HIS9 4.1 0.0 1.0 CA A:CYS102 4.1 0.0 1.0 H A:ARG8 4.1 0.0 1.0 HA A:CYS7 4.2 0.0 1.0 NE2 A:HIS9 4.2 0.0 1.0 CD2 A:HIS9 4.2 0.0 1.0 HB3 A:CYS102 4.3 0.0 1.0 HG13 A:VAL101 4.3 0.0 1.0 HA A:CYS102 4.3 0.0 1.0 N A:HIS9 4.3 0.0 1.0 HB3 A:CYS7 4.3 0.0 1.0 CA A:CYS7 4.4 0.0 1.0 HD23 A:LEU88 4.4 0.0 1.0 CA A:HIS9 4.4 0.0 1.0 HG23 A:VAL106 4.7 0.0 1.0 N A:ARG8 4.8 0.0 1.0 C A:VAL101 4.8 0.0 1.0 HG22 A:VAL106 4.8 0.0 1.0 HD11 A:LEU88 4.9 0.0 1.0 CA A:CYS99 4.9 0.0 1.0 C A:CYS7 5.0 0.0 1.0 H A:VAL101 5.0 0.0 1.0

M.T.Pai, S.R.Tzeng, J.J.Kovacs, M.A.Keaton, S.S.Li, T.P.Yao, P.Zhou. Solution Structure of the Ubp-M Buz Domain, A Highly Specific Protein Module That Recognizes the C-Terminal Tail of Free Ubiquitin. J.Mol.Biol. V. 370 290 2007.
ISSN: ISSN 0022-2836
PubMed: 17512543
DOI: 10.1016/J.JMB.2007.04.015