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

Enzymatic activity of F-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1

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

Protein crystallography data

The structure of F-Degron Fused Zz-Domain of the Arabidopsis Thaliana E3 Ubiquitin- Protein Ligase PRT1, PDB code: 8zga 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) 42.83 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.729, 86.439, 89.769, 90, 90, 90
R / Rfree (%) 25.7 / 29.5

Other elements in 8zga:

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

Zinc (Zn) 12 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 8zga

Go back to Magnesium Binding Sites List in 8zga
Magnesium binding site 1 out of 2 in the F-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 F-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:23.8
occ:1.00
O C:TYR317 2.0 41.2 1.0
O A:TYR317 2.1 39.7 1.0
HD2 C:PRO318 3.0 59.8 1.0
C C:TYR317 3.0 50.4 1.0
C A:TYR317 3.4 42.2 1.0
H C:TYR317 3.4 60.4 1.0
H A:TYR317 3.4 47.3 1.0
CD C:PRO318 3.7 49.9 1.0
HB3 A:TYR317 3.7 63.5 1.0
N C:PRO318 3.7 41.1 1.0
HD1 A:TYR317 3.8 51.2 1.0
HD3 C:PRO318 3.9 59.8 1.0
N C:TYR317 4.0 50.3 1.0
CA C:TYR317 4.1 49.5 1.0
N A:TYR317 4.1 39.4 1.0
CA A:TYR317 4.1 37.6 1.0
HD2 A:PRO318 4.1 49.4 1.0
N A:PRO318 4.3 48.4 1.0
CB A:TYR317 4.4 52.9 1.0
HG23 C:VAL316 4.4 59.0 1.0
HD3 A:PRO318 4.4 49.4 1.0
O D:TYR317 4.5 33.5 1.0
CD A:PRO318 4.5 41.1 1.0
HB3 C:TYR317 4.5 57.6 1.0
HD1 C:TYR317 4.6 60.8 1.0
CD1 A:TYR317 4.7 42.6 1.0
O C:PRO318 4.7 44.0 1.0
HD1 D:TYR317 4.8 52.0 1.0
HG22 C:VAL316 4.8 59.0 1.0
O C:HOH502 4.8 34.9 1.0
O A:HOH501 4.8 39.7 1.0
HA C:TYR317 4.8 59.4 1.0
CB C:TYR317 4.9 48.0 1.0

Magnesium binding site 2 out of 2 in 8zga

Go back to Magnesium Binding Sites List in 8zga
Magnesium binding site 2 out of 2 in the F-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 F-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:128.3
occ:1.00
O B:TYR317 2.0 57.6 1.0
C B:TYR317 3.2 45.7 1.0
HD2 B:PRO318 3.3 52.0 1.0
H B:TYR317 3.5 58.7 1.0
CD B:PRO318 3.9 43.4 1.0
N B:PRO318 3.9 59.7 1.0
HD3 B:PRO318 4.0 52.0 1.0
N B:TYR317 4.2 48.9 1.0
CA B:TYR317 4.3 44.5 1.0
HB3 B:TYR317 4.4 50.0 1.0
HD1 B:TYR317 4.4 74.5 1.0
HG23 B:VAL316 4.7 68.2 1.0
CB B:TYR317 4.9 41.7 1.0

Reference:

W.S.Yang, H.K.Song. Structural Basis For the Recognition of Type-2 N-Degron By PRT1 Plant N-Recognin To Be Published.
Page generated: Fri Aug 15 22:22:57 2025

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