Zinc in PDB 8zg8: Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1

All present enzymatic activity of Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1:
2.3.2.27;

The structure of Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1, PDB code: 8zg8 was solved by W.S.Yang, H.K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.77 / 1.74
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.03, 78.03, 70.452, 90, 90, 120
R / Rfree (%)	23.5 / 27.9

The binding sites of Zinc atom in the Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1 (pdb code 8zg8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1, PDB code: 8zg8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:32.4 occ:0.79 SG A:CYS311 2.3 28.4 1.0 SG A:CYS314 2.3 28.7 1.0 SG A:CYS338 2.3 31.1 1.0 SG A:CYS341 2.4 32.1 1.0 HB2 A:CYS341 2.9 42.1 1.0 H A:CYS314 3.0 37.2 1.0 HB3 A:CYS314 3.1 35.1 1.0 CB A:CYS311 3.1 24.9 1.0 HB3 A:CYS311 3.2 29.9 1.0 HB2 A:CYS311 3.2 29.9 1.0 H A:CYS338 3.2 33.9 1.0 CB A:CYS341 3.2 35.1 1.0 CB A:CYS314 3.3 29.2 1.0 HB3 A:CYS338 3.4 35.4 1.0 HB3 A:SER313 3.4 40.5 1.0 CB A:CYS338 3.5 29.5 1.0 H A:CYS341 3.7 42.8 1.0 N A:CYS314 3.7 31.1 1.0 HG13 A:VAL316 3.7 36.5 1.0 HB3 A:CYS341 3.8 42.1 1.0 N A:CYS338 4.0 28.2 1.0 CA A:CYS314 4.0 35.7 1.0 HB2 A:CYS314 4.1 35.1 1.0 HG11 A:VAL316 4.1 36.5 1.0 N A:CYS341 4.3 35.6 1.0 HB2 A:CYS338 4.3 35.4 1.0 CA A:CYS338 4.3 25.1 1.0 H A:SER313 4.3 38.0 1.0 CA A:CYS341 4.4 37.9 1.0 CG1 A:VAL316 4.4 30.4 1.0 CB A:SER313 4.4 33.7 1.0 H A:VAL316 4.4 36.8 1.0 H A:GLY315 4.5 36.6 1.0 CA A:CYS311 4.5 22.8 1.0 HB2 A:ASP340 4.6 46.0 1.0 HA A:LEU337 4.7 29.8 1.0 C A:SER313 4.7 34.4 1.0 HB A:VAL316 4.7 38.4 1.0 HA A:CYS341 4.8 45.5 1.0 C A:CYS314 4.8 29.4 1.0 HA A:CYS311 4.8 27.4 1.0 HA A:CYS314 4.8 42.8 1.0 HD22 A:LEU337 4.9 40.6 1.0 C A:CYS338 4.9 29.6 1.0 N A:GLY315 4.9 30.5 1.0 HB2 A:SER313 4.9 40.5 1.0 O A:CYS338 4.9 32.5 1.0 CA A:SER313 4.9 32.5 1.0 O A:HOH533 5.0 39.9 1.0 N A:SER313 5.0 31.6 1.0

Zinc binding site 2 out of 2 in the Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin-Protein Ligase PRT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:49.5 occ:0.80 ND1 A:HIS356 2.0 46.5 1.0 ND1 A:HIS360 2.0 62.3 1.0 SG A:CYS329 2.3 45.9 1.0 SG A:CYS326 2.3 45.2 1.0 H A:CYS329 2.7 83.5 1.0 CE1 A:HIS356 2.8 47.5 1.0 CE1 A:HIS360 2.9 71.1 1.0 HE1 A:HIS356 3.0 57.0 1.0 HB3 A:HIS360 3.0 72.0 1.0 CG A:HIS356 3.0 47.0 1.0 CG A:HIS360 3.1 58.2 1.0 HE1 A:HIS360 3.1 85.4 1.0 HB2 A:CYS329 3.1 59.8 1.0 HA A:HIS356 3.1 62.8 1.0 HB2 A:HIS356 3.2 58.6 1.0 CB A:CYS329 3.3 49.9 1.0 CB A:CYS326 3.3 38.6 1.0 HB2 A:CYS326 3.4 46.3 1.0 HB3 A:CYS326 3.4 46.3 1.0 CB A:HIS360 3.4 60.0 1.0 N A:CYS329 3.5 69.6 1.0 CB A:HIS356 3.5 48.9 1.0 HB2 A:ASP328 3.5 76.7 1.0 HB3 A:TYR335 3.6 44.3 1.0 HB2 A:HIS360 3.6 72.0 1.0 CA A:HIS356 3.7 52.3 1.0 CA A:CYS329 3.9 58.6 1.0 NE2 A:HIS356 4.0 44.8 1.0 NE2 A:HIS360 4.1 77.1 1.0 HB3 A:CYS329 4.1 59.8 1.0 CD2 A:HIS356 4.1 45.9 1.0 HB2 A:TYR335 4.1 44.3 1.0 CD2 A:HIS360 4.2 61.2 1.0 CB A:TYR335 4.2 36.9 1.0 HA A:CYS329 4.3 70.4 1.0 HB3 A:HIS356 4.4 58.6 1.0 H A:ASP328 4.4 73.3 1.0 H A:THR357 4.5 84.3 1.0 CB A:ASP328 4.5 63.9 1.0 C A:ASP328 4.6 69.7 1.0 CG A:TYR335 4.6 36.1 1.0 N A:HIS356 4.7 59.6 1.0 CA A:CYS326 4.7 32.4 1.0 HD1 A:TYR335 4.7 43.7 1.0 HE2 A:HIS356 4.7 53.7 1.0 C A:HIS356 4.8 67.4 1.0 O A:GLN355 4.8 66.9 1.0 HE2 A:HIS360 4.8 92.5 1.0 CA A:ASP328 4.9 66.5 1.0 CD1 A:TYR335 4.9 36.4 1.0 HB3 A:ASP328 4.9 76.7 1.0 CA A:HIS360 4.9 68.6 1.0 HA A:CYS326 4.9 38.9 1.0 N A:THR357 4.9 70.2 1.0 N A:ASP328 4.9 61.1 1.0 HD2 A:HIS356 5.0 55.0 1.0

W.S.Yang, H.K.Song. Structural Basis For the Recognition of Type-2 N-Degron By PRT1 Plant N-Recognin To Be Published.