Zinc in PDB 3b08: 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: 3b08 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)	46.93 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.938, 104.938, 170.410, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.1

The binding sites of Zinc atom in the Crystal Structure of the Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin (pdb code 3b08). 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 Mouse HOIL1-L-Nzf in Complex with Linear Di- Ubiquitin, PDB code: 3b08:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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:23.4 occ:1.00 SG B:CYS200 2.3 13.3 1.0 SG B:CYS214 2.4 15.4 1.0 SG B:CYS211 2.4 12.2 1.0 SG B:CYS197 2.4 14.0 1.0 CB B:CYS197 3.1 13.7 1.0 CB B:CYS211 3.2 13.7 1.0 CB B:CYS200 3.4 14.3 1.0 CB B:CYS214 3.4 13.2 1.0 N B:CYS214 3.8 11.6 1.0 N B:CYS200 3.8 15.4 1.0 CA B:CYS214 4.1 11.3 1.0 CA B:CYS200 4.1 12.6 1.0 CB B:MET213 4.5 12.6 1.0 O B:HOH309 4.6 35.8 1.0 CA B:CYS197 4.6 12.3 1.0 CA B:CYS211 4.6 12.5 1.0 C B:CYS214 4.7 16.5 1.0 CB B:ARG216 4.8 14.1 1.0 C B:MET213 4.8 14.2 1.0 CB B:PHE202 4.8 12.9 1.0 C B:CYS200 4.8 11.7 1.0 C B:GLY199 4.8 18.9 1.0 N B:THR201 4.9 11.9 1.0 N B:CYS215 5.0 14.9 1.0

Zinc binding site 2 out of 4 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:23.6 occ:1.00 SG E:CYS200 2.3 13.7 1.0 SG E:CYS214 2.3 14.4 1.0 SG E:CYS197 2.4 13.7 1.0 SG E:CYS211 2.4 12.7 1.0 CB E:CYS197 3.1 11.0 1.0 CB E:CYS211 3.2 12.2 1.0 CB E:CYS200 3.4 13.6 1.0 CB E:CYS214 3.4 13.4 1.0 N E:CYS200 3.7 11.8 1.0 N E:CYS214 3.8 15.2 1.0 CA E:CYS200 4.1 11.5 1.0 CA E:CYS214 4.1 15.8 1.0 CA E:CYS197 4.5 8.5 1.0 CB E:MET213 4.6 12.7 1.0 CA E:CYS211 4.6 9.0 1.0 C E:GLY199 4.7 20.5 1.0 CB E:ARG216 4.8 11.2 1.0 C E:CYS214 4.8 16.0 1.0 C E:CYS200 4.8 10.8 1.0 O E:HOH251 4.8 30.5 1.0 C E:MET213 4.8 14.2 1.0 CB E:PHE202 4.8 11.4 1.0 N E:THR201 4.9 10.9 1.0 CA E:GLY199 4.9 18.4 1.0

Zinc binding site 3 out of 4 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 3 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 H:Zn1 b:21.0 occ:1.00 SG H:CYS214 2.3 11.8 1.0 SG H:CYS200 2.3 12.1 1.0 SG H:CYS197 2.4 12.2 1.0 SG H:CYS211 2.4 10.4 1.0 CB H:CYS197 3.1 11.8 1.0 CB H:CYS211 3.2 10.4 1.0 CB H:CYS214 3.4 11.3 1.0 CB H:CYS200 3.4 10.0 1.0 N H:CYS200 3.8 12.3 1.0 N H:CYS214 3.8 10.5 1.0 CA H:CYS214 4.1 12.0 1.0 CA H:CYS200 4.1 9.7 1.0 O H:HOH256 4.5 28.8 1.0 CA H:CYS197 4.6 10.0 1.0 CB H:MET213 4.6 11.8 1.0 CA H:CYS211 4.6 10.0 1.0 C H:CYS214 4.7 15.3 1.0 CB H:ARG216 4.8 11.8 1.0 C H:GLY199 4.8 16.2 1.0 C H:MET213 4.8 14.9 1.0 C H:CYS200 4.9 10.6 1.0 CB H:PHE202 4.9 9.2 1.0 N H:THR201 4.9 10.4 1.0 N H:CYS215 5.0 13.6 1.0

Zinc binding site 4 out of 4 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 4 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 K:Zn1 b:21.8 occ:1.00 SG K:CYS200 2.3 11.5 1.0 SG K:CYS214 2.3 12.3 1.0 SG K:CYS197 2.4 12.2 1.0 SG K:CYS211 2.4 10.2 1.0 CB K:CYS197 3.1 10.3 1.0 CB K:CYS211 3.2 12.0 1.0 CB K:CYS200 3.4 15.0 1.0 CB K:CYS214 3.4 14.1 1.0 N K:CYS214 3.8 10.6 1.0 N K:CYS200 3.8 11.0 1.0 CA K:CYS214 4.1 9.9 1.0 CA K:CYS200 4.1 9.2 1.0 CB K:MET213 4.5 13.3 1.0 CA K:CYS197 4.5 11.2 1.0 O K:HOH90 4.6 30.5 1.0 CA K:CYS211 4.6 11.5 1.0 C K:CYS214 4.7 13.9 1.0 CB K:ARG216 4.7 12.1 1.0 C K:MET213 4.8 13.3 1.0 C K:GLY199 4.8 16.4 1.0 C K:CYS200 4.8 10.2 1.0 CB K:PHE202 4.8 11.0 1.0 N K:THR201 4.9 12.5 1.0 N K:CYS215 5.0 11.2 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