Zinc in PDB 1o06: Crystal Structure of the VPS27P Ubiquitin Interacting Motif (Uim)

The structure of Crystal Structure of the VPS27P Ubiquitin Interacting Motif (Uim), PDB code: 1o06 was solved by R.D.Fisher, B.Wang, S.L.Alam, D.S.Higginson, R.Rich, D.Myszka, W.I.Sundquist, C.P.Hill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.29 / 1.45
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	34.967, 34.967, 64.243, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 22.4

The binding sites of Zinc atom in the Crystal Structure of the VPS27P Ubiquitin Interacting Motif (Uim) (pdb code 1o06). 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 VPS27P Ubiquitin Interacting Motif (Uim), PDB code: 1o06:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the VPS27P Ubiquitin Interacting Motif (Uim)


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 VPS27P Ubiquitin Interacting Motif (Uim) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:10.9 occ:1.00 OD2 A:ASP5 1.9 10.4 1.0 CG A:ASP5 2.7 10.4 1.0 OD1 A:ASP5 2.7 12.2 1.0 ZN A:ZN102 3.5 8.9 0.2 CB A:ASP5 4.1 9.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the VPS27P Ubiquitin Interacting Motif (Uim)


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 VPS27P Ubiquitin Interacting Motif (Uim) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:8.9 occ:0.25 OD2 A:ASP5 2.3 10.4 1.0 CG A:ASP5 3.2 10.4 1.0 CB A:ASP5 3.4 9.2 1.0 ZN A:ZN101 3.5 10.9 1.0 OD1 A:ASP5 4.3 12.2 1.0 O A:HOH210 4.9 22.5 1.0 CA A:ASP5 4.9 9.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the VPS27P Ubiquitin Interacting Motif (Uim)


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 VPS27P Ubiquitin Interacting Motif (Uim) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:14.4 occ:0.50 ZN A:ZN103 0.0 14.4 0.5 ZN A:ZN103 0.9 18.4 0.5 N A:GLU1 1.8 20.7 1.0 CA A:GLU1 2.9 21.1 1.0 C A:GLU1 3.3 19.9 1.0 O A:GLU1 3.7 20.6 1.0 N A:GLU2 3.8 18.6 1.0 CB A:GLU1 4.2 21.8 1.0 O A:HOH209 4.2 10.8 0.5 CG A:GLU2 4.6 17.9 1.0 O A:HOH217 4.8 17.1 0.5 CA A:GLU2 4.9 17.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the VPS27P Ubiquitin Interacting Motif (Uim)


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 VPS27P Ubiquitin Interacting Motif (Uim) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:18.4 occ:0.50 ZN A:ZN103 0.0 18.4 0.5 ZN A:ZN103 0.9 14.4 0.5 N A:GLU1 2.5 20.7 1.0 CA A:GLU1 3.4 21.1 1.0 C A:GLU1 3.5 19.9 1.0 O A:HOH209 3.5 10.8 0.5 N A:GLU2 3.8 18.6 1.0 O A:GLU1 3.8 20.6 1.0 O A:HOH217 4.1 17.1 0.5 CG A:GLU2 4.1 17.9 1.0 CA A:GLU2 4.7 17.5 1.0 OE2 A:GLU2 4.7 18.9 1.0 CB A:GLU1 4.8 21.8 1.0 CD A:GLU2 5.0 19.4 1.0

R.D.Fisher, B.Wang, S.L.Alam, D.S.Higginson, H.Robinson, W.I.Sundquist, C.P.Hill. Structure and Ubiquitin Binding of the Ubiquitin-Interacting Motif. J.Biol.Chem. V. 278 28976 2003.
ISSN: ISSN 0021-9258
PubMed: 12750381
DOI: 10.1074/JBC.M302596200