Zinc in PDB 8zgb: W-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1

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

The structure of W-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1, PDB code: 8zgb 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)	40.77 / 2.79
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.26, 106.26, 97.063, 90, 90, 90
R / Rfree (%)	23.5 / 26.1

The binding sites of Zinc atom in the W-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1 (pdb code 8zgb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the W-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1, PDB code: 8zgb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the W-Degron Fused 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 W-Degron Fused 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:128.4 occ:1.00 ND1 A:HIS356 2.0 127.8 1.0 ND1 A:HIS360 2.0 148.9 1.0 SG A:CYS329 2.3 132.4 1.0 SG A:CYS326 2.4 115.2 1.0 H A:CYS329 2.8 189.0 1.0 CE1 A:HIS356 2.8 124.4 1.0 HB2 A:CYS329 2.9 167.6 1.0 HB3 A:HIS360 2.9 158.9 1.0 CG A:HIS360 3.0 142.1 1.0 HE1 A:HIS356 3.0 149.8 1.0 CE1 A:HIS360 3.0 140.5 1.0 CG A:HIS356 3.1 128.1 1.0 CB A:CYS329 3.1 139.2 1.0 HA A:HIS356 3.1 152.8 1.0 HB2 A:HIS356 3.2 145.2 1.0 HE1 A:HIS360 3.2 169.1 1.0 CB A:HIS360 3.3 132.1 1.0 HB2 A:HIS360 3.3 158.9 1.0 N A:CYS329 3.3 157.1 1.0 CB A:CYS326 3.4 126.2 1.0 HB2 A:CYS326 3.4 151.9 1.0 HB3 A:CYS326 3.5 151.9 1.0 CB A:HIS356 3.5 120.6 1.0 CA A:CYS329 3.7 151.7 1.0 HB2 A:ASP328 3.7 173.1 1.0 CA A:HIS356 3.8 127.0 1.0 HB3 A:TYR335 3.8 128.9 1.0 HA A:CYS329 3.8 182.5 1.0 HB3 A:CYS329 3.9 167.6 1.0 NE2 A:HIS356 4.0 110.1 1.0 CD2 A:HIS356 4.1 110.2 1.0 CD2 A:HIS360 4.1 146.2 1.0 NE2 A:HIS360 4.1 153.3 1.0 HD2 A:TYR335 4.2 146.4 1.0 H A:THR357 4.2 181.2 1.0 CD2 A:TYR335 4.3 121.6 1.0 HB2 A:TYR335 4.3 128.9 1.0 H A:ASP328 4.3 158.7 1.0 CG A:TYR335 4.3 108.3 1.0 CB A:TYR335 4.4 107.0 1.0 C A:ASP328 4.4 167.4 1.0 HB3 A:HIS356 4.4 145.2 1.0 CB A:ASP328 4.5 143.8 1.0 O A:GLN355 4.6 134.0 1.0 C A:HIS356 4.7 151.6 1.0 HB3 A:ASP328 4.7 173.1 1.0 N A:THR357 4.7 150.6 1.0 HE2 A:HIS356 4.7 129.6 1.0 CA A:HIS360 4.8 146.1 1.0 CA A:CYS326 4.8 128.5 1.0 CA A:ASP328 4.8 140.2 1.0 N A:HIS356 4.9 122.9 1.0 CE2 A:TYR335 4.9 141.3 1.0 HE2 A:HIS360 4.9 184.5 1.0 N A:ASP328 4.9 131.8 1.0 HD2 A:HIS360 5.0 176.0 1.0 HD2 A:HIS356 5.0 129.8 1.0

Zinc binding site 2 out of 4 in the W-Degron Fused 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 W-Degron Fused 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:132.7 occ:1.00 SG A:CYS314 2.3 100.3 1.0 SG A:CYS341 2.3 128.1 1.0 SG A:CYS311 2.3 112.9 1.0 SG A:CYS338 2.3 118.4 1.0 HB2 A:CYS341 2.8 151.0 1.0 CB A:CYS341 3.1 125.4 1.0 H A:CYS338 3.1 142.2 1.0 H A:CYS314 3.3 127.8 1.0 HB2 A:CYS311 3.3 137.7 1.0 CB A:CYS311 3.3 114.3 1.0 HB3 A:CYS314 3.3 125.5 1.0 HB3 A:CYS311 3.4 137.7 1.0 H A:CYS341 3.4 172.4 1.0 CB A:CYS314 3.5 104.2 1.0 HB3 A:CYS338 3.5 119.6 1.0 CB A:CYS338 3.6 99.2 1.0 HB3 A:SER313 3.7 152.3 1.0 HB3 A:CYS341 3.7 151.0 1.0 HG12 A:VAL316 3.8 121.5 1.0 HG11 A:VAL316 3.8 121.5 1.0 N A:CYS338 3.9 118.1 1.0 N A:CYS314 3.9 106.1 1.0 N A:CYS341 4.1 143.2 1.0 CA A:CYS341 4.2 119.5 1.0 HB2 A:CYS314 4.2 125.5 1.0 CA A:CYS338 4.3 120.8 1.0 CG1 A:VAL316 4.3 100.8 1.0 CA A:CYS314 4.3 113.5 1.0 HB2 A:CYS338 4.3 119.6 1.0 HD22 A:LEU337 4.4 180.3 1.0 H A:SER313 4.5 171.2 1.0 H A:VAL316 4.5 132.1 1.0 HB2 A:ASP340 4.5 167.6 1.0 HA A:CYS341 4.6 143.8 1.0 CB A:SER313 4.6 126.5 1.0 HA A:LEU337 4.7 149.8 1.0 HB3 A:LEU337 4.7 154.5 1.0 C A:CYS338 4.7 113.5 1.0 O A:CYS338 4.8 111.5 1.0 HB A:VAL316 4.8 112.8 1.0 CA A:CYS311 4.8 129.2 1.0 HD23 A:LEU337 4.9 180.3 1.0 H A:GLY315 4.9 161.3 1.0 C A:SER313 5.0 119.9 1.0

Zinc binding site 3 out of 4 in the W-Degron Fused 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 3 of W-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:124.9 occ:1.00 ND1 B:HIS360 2.0 135.3 1.0 ND1 B:HIS356 2.0 112.2 1.0 SG B:CYS329 2.2 119.0 1.0 SG B:CYS326 2.3 115.1 1.0 HB2 B:CYS329 2.8 172.5 1.0 CE1 B:HIS360 2.9 144.9 1.0 CE1 B:HIS356 2.9 113.8 1.0 CB B:CYS329 3.0 143.3 1.0 HA B:HIS356 3.0 185.7 1.0 H B:CYS329 3.0 157.3 1.0 HE1 B:HIS360 3.1 174.4 1.0 HE1 B:HIS356 3.1 137.1 1.0 HB3 B:HIS360 3.1 147.4 1.0 CG B:HIS360 3.1 120.6 1.0 CG B:HIS356 3.1 136.0 1.0 HB2 B:HIS356 3.2 148.8 1.0 CB B:CYS326 3.3 137.2 1.0 HB2 B:CYS326 3.3 165.1 1.0 HB3 B:CYS326 3.3 165.1 1.0 N B:CYS329 3.5 130.7 1.0 CB B:HIS360 3.5 122.4 1.0 CB B:HIS356 3.5 123.6 1.0 CA B:CYS329 3.6 145.8 1.0 HB2 B:HIS360 3.7 147.4 1.0 HA B:CYS329 3.7 175.5 1.0 CA B:HIS356 3.7 154.3 1.0 HB3 B:TYR335 3.8 183.6 1.0 HB3 B:CYS329 3.8 172.5 1.0 NE2 B:HIS360 4.1 137.7 1.0 H B:THR357 4.1 177.8 1.0 NE2 B:HIS356 4.1 127.2 1.0 HB2 B:ASP328 4.1 163.1 1.0 HB2 B:TYR335 4.1 183.6 1.0 CD2 B:HIS360 4.2 133.3 1.0 CD2 B:HIS356 4.2 115.6 1.0 CB B:TYR335 4.3 152.6 1.0 H B:ASP328 4.4 165.9 1.0 HB3 B:HIS356 4.5 148.8 1.0 C B:ASP328 4.5 153.3 1.0 CG B:TYR335 4.6 105.9 1.0 N B:THR357 4.7 147.7 1.0 C B:HIS356 4.7 137.3 1.0 HD2 B:TYR335 4.7 109.8 1.0 CA B:CYS326 4.7 140.3 1.0 N B:HIS356 4.8 170.1 1.0 CD2 B:TYR335 4.8 91.1 1.0 O B:GLN355 4.8 140.2 1.0 HE2 B:HIS360 4.8 165.7 1.0 HE2 B:HIS356 4.9 153.1 1.0 CB B:ASP328 4.9 135.5 1.0 HA B:CYS326 4.9 168.9 1.0 CA B:HIS360 4.9 157.6 1.0 N B:ASP328 5.0 137.9 1.0

Zinc binding site 4 out of 4 in the W-Degron Fused 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 4 of W-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:118.8 occ:1.00 SG B:CYS341 2.2 124.9 1.0 SG B:CYS338 2.3 116.6 1.0 SG B:CYS311 2.4 107.3 1.0 SG B:CYS314 2.4 117.7 1.0 HB2 B:CYS341 2.7 165.9 1.0 CB B:CYS341 3.1 137.9 1.0 H B:CYS338 3.1 162.3 1.0 H B:CYS314 3.1 144.4 1.0 HB2 B:CYS311 3.2 148.5 1.0 CB B:CYS311 3.2 123.3 1.0 HB3 B:CYS314 3.3 118.0 1.0 HB3 B:CYS311 3.3 148.5 1.0 HB3 B:CYS338 3.4 140.6 1.0 HB3 B:SER313 3.4 169.4 1.0 H B:CYS341 3.4 165.6 1.0 CB B:CYS314 3.4 98.0 1.0 CB B:CYS338 3.5 116.7 1.0 HB3 B:CYS341 3.7 165.9 1.0 N B:CYS314 3.8 120.0 1.0 N B:CYS338 3.9 134.8 1.0 HG12 B:VAL316 4.0 139.2 1.0 HG11 B:VAL316 4.0 139.2 1.0 N B:CYS341 4.0 137.6 1.0 CA B:CYS341 4.2 146.5 1.0 HB2 B:CYS314 4.2 118.0 1.0 CA B:CYS314 4.2 135.7 1.0 CA B:CYS338 4.2 126.9 1.0 HB2 B:CYS338 4.3 140.6 1.0 H B:SER313 4.3 147.2 1.0 HD22 B:LEU337 4.3 141.9 1.0 CB B:SER313 4.3 140.7 1.0 HB2 B:ASP340 4.4 192.4 1.0 CG1 B:VAL316 4.5 115.6 1.0 HA B:LEU337 4.5 127.3 1.0 HA B:CYS341 4.6 176.3 1.0 H B:VAL316 4.6 115.9 1.0 CA B:CYS311 4.7 109.1 1.0 C B:SER313 4.7 109.7 1.0 HG B:SER313 4.8 181.2 1.0 C B:CYS338 4.8 142.6 1.0 OG B:SER313 4.8 150.6 1.0 O B:CYS338 4.9 138.3 1.0 HB B:VAL316 4.9 146.3 1.0 H B:GLY315 4.9 117.3 1.0 HA B:CYS311 4.9 131.4 1.0 N B:SER313 4.9 122.2 1.0 CA B:SER313 4.9 118.9 1.0 HB3 B:LEU337 4.9 149.7 1.0 HB2 B:SER313 4.9 169.4 1.0 HA B:CYS314 5.0 163.3 1.0 C B:LEU337 5.0 120.2 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.