Zinc in PDB 3b0a: Crystal Structure of the Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin

The structure of Crystal Structure of the Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin, PDB code: 3b0a was solved by Y.Sato, H.Fujita, A.Yoshikawa, M.Yamashita, A.Yamagata, S.E.Kaiser, K.Iwai, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.44 / 1.90
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	113.650, 113.650, 75.663, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 22.7

The binding sites of Zinc atom in the Crystal Structure of the Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin (pdb code 3b0a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin, PDB code: 3b0a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin


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 Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:37.8 occ:1.00 SG B:CYS200 2.2 26.3 1.0 SG B:CYS214 2.3 26.3 1.0 SG B:CYS211 2.4 25.4 1.0 SG B:CYS197 2.4 26.0 1.0 CB B:CYS197 3.0 21.9 1.0 CB B:CYS211 3.2 22.4 1.0 CB B:CYS200 3.3 28.4 1.0 CB B:CYS214 3.3 25.7 1.0 N B:CYS200 3.7 26.4 1.0 N B:CYS214 3.8 27.6 1.0 CA B:CYS214 4.1 31.3 1.0 CA B:CYS200 4.1 25.9 1.0 CA B:CYS197 4.4 21.1 1.0 CB B:MET213 4.5 21.1 1.0 CA B:CYS211 4.7 23.9 1.0 C B:GLY199 4.7 32.1 1.0 C B:CYS214 4.7 31.0 1.0 CB B:ARG216 4.7 26.7 1.0 O B:HOH92 4.7 36.1 1.0 C B:MET213 4.8 28.9 1.0 CB B:PHE202 4.8 25.9 1.0 C B:CYS200 4.8 25.9 1.0 CA B:GLY199 4.9 24.1 1.0 C B:CYS197 4.9 21.1 1.0 N B:THR201 4.9 27.3 1.0 N B:ARG216 4.9 22.6 1.0 N B:CYS215 5.0 24.0 1.0 N B:GLY199 5.0 24.6 1.0 O B:CYS197 5.0 22.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin


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 Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1 b:38.7 occ:1.00 SG E:CYS214 2.3 28.7 1.0 SG E:CYS200 2.3 25.7 1.0 SG E:CYS197 2.4 26.6 1.0 SG E:CYS211 2.4 26.2 1.0 CB E:CYS197 3.0 20.7 1.0 CB E:CYS211 3.1 25.0 1.0 CB E:CYS214 3.4 29.3 1.0 CB E:CYS200 3.4 28.2 1.0 N E:CYS214 3.8 28.7 1.0 N E:CYS200 3.8 30.6 1.0 CA E:CYS214 4.1 27.6 1.0 CA E:CYS200 4.2 29.9 1.0 CA E:CYS197 4.5 24.5 1.0 CA E:CYS211 4.6 25.0 1.0 CB E:MET213 4.6 30.2 1.0 C E:CYS214 4.7 28.1 1.0 CB E:ARG216 4.8 35.3 1.0 C E:GLY199 4.8 32.9 1.0 CB E:PHE202 4.8 22.3 1.0 C E:MET213 4.8 29.1 1.0 C E:CYS200 4.9 29.2 1.0 N E:THR201 4.9 27.0 1.0 N E:CYS215 4.9 29.1 1.0 N E:ARG216 5.0 27.0 1.0 CA E:GLY199 5.0 28.2 1.0

Y.Sato, H.Fujita, A.Yoshikawa, M.Yamashita, A.Yamagata, S.E.Kaiser, K.Iwai, S.Fukai. Specific Recognition of Linear Ubiquitin Chains By the NPL4 Zinc Finger (Nzf) Domain of the Hoil-1L Subunit of the Linear Ubiquitin Chain Assembly Complex Proc.Natl.Acad.Sci.Usa V. 108 20520 2011.
ISSN: ISSN 0027-8424
PubMed: 22139374
DOI: 10.1073/PNAS.1109088108