Zinc in PDB 3wwq: Crystal Structure of FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin

The structure of Crystal Structure of FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin, PDB code: 3wwq was solved by Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.767, 45.850, 172.900, 90.00, 98.06, 90.00
R / Rfree (%)	20.8 / 23.5

The binding sites of Zinc atom in the Crystal Structure of FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin (pdb code 3wwq). 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 FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin, PDB code: 3wwq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin


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 FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.5 occ:1.00 NE2 C:HIS166 2.0 27.3 1.0 SG C:CYS170 2.3 26.3 1.0 SG C:CYS147 2.3 26.4 1.0 SG C:CYS150 2.3 27.6 1.0 CD2 C:HIS166 3.0 25.9 1.0 CB C:CYS147 3.1 28.3 1.0 CE1 C:HIS166 3.1 27.7 1.0 CB C:CYS150 3.2 30.1 1.0 CB C:CYS170 3.4 25.3 1.0 N C:CYS150 3.7 30.6 1.0 CA C:CYS150 4.0 30.4 1.0 ND1 C:HIS166 4.1 25.8 1.0 CG C:HIS166 4.1 25.1 1.0 CA C:CYS147 4.5 28.7 1.0 CB C:MET149 4.5 27.7 1.0 C C:MET149 4.7 30.6 1.0 C C:CYS150 4.7 33.4 1.0 CA C:CYS170 4.7 24.8 1.0 O C:HIS166 4.8 22.6 1.0 CB C:LYS152 4.9 40.0 1.0 N C:MET149 4.9 29.7 1.0 N C:GLN151 4.9 34.8 1.0 CA C:MET149 5.0 29.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin


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 FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:25.1 occ:1.00 NE2 F:HIS166 2.0 28.1 1.0 SG F:CYS170 2.3 27.6 1.0 SG F:CYS147 2.3 28.7 1.0 SG F:CYS150 2.3 31.4 1.0 CD2 F:HIS166 2.9 25.6 1.0 CE1 F:HIS166 3.0 27.7 1.0 CB F:CYS147 3.1 32.3 1.0 CB F:CYS150 3.2 33.7 1.0 CB F:CYS170 3.4 26.6 1.0 N F:CYS150 3.7 32.6 1.0 CA F:CYS150 4.0 34.2 1.0 CG F:HIS166 4.1 25.1 1.0 ND1 F:HIS166 4.1 25.9 1.0 CA F:CYS147 4.6 34.2 1.0 CB F:MET149 4.6 30.9 1.0 O F:HIS166 4.7 22.6 1.0 C F:MET149 4.7 33.1 1.0 C F:CYS150 4.7 36.8 1.0 CA F:CYS170 4.7 25.7 1.0 CB F:LYS152 4.9 45.9 1.0 N F:MET149 4.9 32.8 1.0 N F:GLN151 5.0 37.6 1.0 CA F:MET149 5.0 31.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin


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 FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:28.2 occ:1.00 NE2 I:HIS166 2.0 32.4 1.0 SG I:CYS147 2.3 33.9 1.0 SG I:CYS150 2.3 33.9 1.0 SG I:CYS170 2.3 30.9 1.0 CD2 I:HIS166 3.0 30.1 1.0 CE1 I:HIS166 3.0 32.3 1.0 CB I:CYS147 3.1 36.1 1.0 CB I:CYS150 3.2 35.5 1.0 CB I:CYS170 3.4 30.8 1.0 N I:CYS150 3.7 35.9 1.0 CA I:CYS150 4.0 37.0 1.0 ND1 I:HIS166 4.1 30.1 1.0 CG I:HIS166 4.1 28.7 1.0 CA I:CYS147 4.5 37.8 1.0 CB I:MET149 4.5 36.4 1.0 C I:MET149 4.7 37.5 1.0 C I:CYS150 4.7 38.9 1.0 CA I:CYS170 4.8 29.2 1.0 O I:HIS166 4.8 25.2 1.0 CB I:LYS152 4.9 51.9 1.0 N I:GLN151 4.9 40.8 1.0 N I:MET149 5.0 38.4 1.0 CA I:MET149 5.0 37.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin


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 FAAP20 Ubz Domain in Complex with LYS63-Linked Diubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn201 b:28.8 occ:1.00 NE2 L:HIS166 2.0 32.2 1.0 SG L:CYS147 2.3 34.1 1.0 SG L:CYS170 2.3 28.9 1.0 SG L:CYS150 2.3 29.4 1.0 CD2 L:HIS166 2.9 30.6 1.0 CE1 L:HIS166 3.1 31.4 1.0 CB L:CYS147 3.1 36.3 1.0 CB L:CYS150 3.2 32.1 1.0 CB L:CYS170 3.4 28.6 1.0 N L:CYS150 3.6 30.9 1.0 CA L:CYS150 4.0 32.6 1.0 CG L:HIS166 4.1 30.6 1.0 ND1 L:HIS166 4.1 31.5 1.0 CB L:MET149 4.5 33.8 1.0 CA L:CYS147 4.6 38.4 1.0 C L:MET149 4.6 33.7 1.0 O L:HIS166 4.7 27.0 1.0 C L:CYS150 4.7 34.5 1.0 CA L:CYS170 4.7 28.3 1.0 N L:MET149 4.9 34.9 1.0 CA L:MET149 4.9 34.3 1.0 CB L:LYS152 5.0 43.0 1.0 N L:GLN151 5.0 35.5 1.0

A.Toma, T.S.Takahashi, Y.Sato, A.Yamagata, S.Goto-Ito, S.Nakada, A.Fukuto, Y.Horikoshi, S.Tashiro, S.Fukai. Structural Basis For Ubiquitin Recognition By Ubiquitin-Binding Zinc Finger of FAAP20 Plos One V. 10 20887 2015.
ISSN: ESSN 1932-6203
PubMed: 25799058
DOI: 10.1371/JOURNAL.PONE.0120887