Magnesium in PDB 8zg9: Y-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1

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

The structure of Y-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1, PDB code: 8zg9 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)	42.98 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.254, 85.737, 85.97, 90, 90, 90
R / Rfree (%)	21.1 / 23.7

The structure of Y-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1 also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

The binding sites of Magnesium atom in the Y-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1 (pdb code 8zg9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Y-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1, PDB code: 8zg9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Y-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y-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:Mg403 b:9.2 occ:1.00 O A:TYR317 2.3 20.7 1.0 C A:TYR317 3.5 15.4 1.0 H A:TYR317 3.6 19.7 1.0 HD2 A:PRO318 3.9 21.0 1.0 HD1 A:TYR317 4.1 17.1 1.0 HB3 A:TYR317 4.2 19.0 1.0 N A:TYR317 4.3 16.4 1.0 CA A:TYR317 4.4 17.5 1.0 N A:PRO318 4.4 16.0 1.0 O A:HOH521 4.5 23.9 1.0 CD A:PRO318 4.5 17.5 1.0 HD3 A:PRO318 4.5 21.0 1.0 O A:HOH514 4.5 17.5 1.0 CB A:TYR317 4.8 15.8 1.0 CD1 A:TYR317 5.0 14.3 1.0

Magnesium binding site 2 out of 2 in the Y-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y-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:Mg403 b:33.0 occ:1.00 O B:HOH517 2.1 27.2 1.0 O B:TYR317 2.1 18.8 1.0 O B:HOH533 2.4 30.3 1.0 O B:HOH528 2.5 28.0 1.0 C B:TYR317 3.3 17.1 1.0 H B:TYR317 3.4 21.8 1.0 HD2 B:PRO318 3.9 20.4 1.0 HB3 B:TYR317 3.9 20.6 1.0 HD1 B:TYR317 3.9 21.8 1.0 N B:TYR317 4.1 18.2 1.0 CA B:TYR317 4.1 17.0 1.0 N B:PRO318 4.2 19.2 1.0 O B:HOH513 4.3 22.1 1.0 CD B:PRO318 4.4 17.0 1.0 HD3 B:PRO318 4.4 20.4 1.0 CB B:TYR317 4.5 17.2 1.0 CD1 B:TYR317 4.7 18.1 1.0 HG21 B:VAL316 4.8 28.1 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.