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Magnesium in PDB 4naa: Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K

Protein crystallography data

The structure of Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K, PDB code: 4naa was solved by X.Yang, X.Zeng, Z.Ren, K.H.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.09 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.521, 77.336, 189.312, 90.00, 95.62, 90.00
R / Rfree (%) 14.7 / 18.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K (pdb code 4naa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K, PDB code: 4naa:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4naa

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Magnesium binding site 1 out of 6 in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:48.6
occ:1.00
 O B:HOH756 2.1 53.4 1.0
O B:HOH755 2.1 48.8 1.0
O A:HOH770 2.1 48.0 1.0
O B:HOH757 2.1 34.0 1.0
O B:HOH691 2.2 39.6 1.0
O A:HOH771 2.3 59.6 1.0
O B:HOH758 3.8 46.9 1.0
O B:HOH800 3.9 58.8 1.0
O B:HOH690 4.2 28.2 1.0
O B:HOH631 4.4 30.3 1.0
O B:HOH839 4.4 57.9 1.0
O A:THR356 4.5 22.6 1.0
O B:HOH630 4.8 33.2 1.0

Magnesium binding site 2 out of 6 in 4naa

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Magnesium binding site 2 out of 6 in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:50.8
occ:1.00
 O A:HOH832 2.0 58.9 1.0
O B:HOH801 2.1 51.0 1.0
O A:HOH793 2.1 55.0 1.0
O A:HOH794 2.3 55.2 1.0
O B:HOH800 2.5 58.8 1.0
O A:HOH718 4.1 33.9 1.0
O A:HOH589 4.3 30.9 1.0
O A:HOH591 4.3 28.3 1.0
O A:HOH590 4.4 30.5 1.0
O B:THR356 4.4 23.1 1.0
O B:HOH691 4.7 39.6 1.0
CB B:THR356 5.0 29.8 1.0

Magnesium binding site 3 out of 6 in 4naa

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Magnesium binding site 3 out of 6 in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:42.8
occ:1.00
 O C:HOH751 2.0 50.2 1.0
O D:HOH765 2.1 45.8 1.0
O C:HOH737 2.1 34.8 1.0
O C:HOH750 2.2 59.0 1.0
O C:HOH738 2.2 39.4 1.0
O C:HOH749 2.3 46.2 1.0
O D:HOH681 4.0 39.7 1.0
O C:HOH901 4.0 57.3 1.0
O D:HOH620 4.4 29.1 1.0
O C:HOH726 4.4 49.5 1.0
O D:HOH621 4.4 30.6 1.0
O C:THR356 4.5 23.7 1.0
O D:HOH689 4.8 30.6 1.0

Magnesium binding site 4 out of 6 in 4naa

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Magnesium binding site 4 out of 6 in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:69.9
occ:1.00
 O D:HOH774 2.1 65.0 1.0
O D:HOH762 2.3 40.9 1.0
O C:HOH748 2.3 51.6 1.0
O C:HOH583 2.4 57.0 1.0
O D:HOH879 2.5 55.4 1.0
O D:HOH763 2.6 49.8 1.0
O C:HOH669 3.8 34.3 1.0
O D:HOH796 3.8 37.2 1.0
O D:HOH764 3.9 57.4 1.0
O C:HOH514 4.2 24.5 1.0
O D:HOH727 4.2 46.3 1.0
O C:HOH513 4.3 33.0 1.0
OD2 C:ASP77 4.4 28.8 1.0
O C:HOH747 4.4 38.5 1.0
O D:HOH529 4.7 26.9 1.0
O C:HOH883 4.7 44.8 1.0
NH2 C:ARG41 4.8 18.6 1.0
CZ C:ARG41 4.8 23.7 1.0
NH1 C:ARG41 4.8 18.1 1.0

Magnesium binding site 5 out of 6 in 4naa

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Magnesium binding site 5 out of 6 in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:56.6
occ:1.00
 O C:HOH827 2.2 46.3 1.0
O C:HOH828 2.2 53.5 1.0
OD2 C:ASP156 2.4 43.4 1.0
O C:HOH778 2.5 41.1 1.0
CG C:ASP156 3.4 37.8 1.0
OD1 C:ASP156 3.7 32.2 1.0
O C:HOH779 3.9 47.3 1.0
O C:HOH832 4.0 52.0 1.0
OE1 C:GLN164 4.1 33.8 1.0
NE2 C:GLN164 4.3 30.1 1.0
CD C:GLN164 4.7 31.6 1.0
CB C:LEU154 4.7 18.4 1.0
CB C:ASP156 4.8 27.3 1.0
O C:LEU154 4.8 25.8 1.0
CD1 C:LEU154 4.8 20.7 1.0
O C:HOH780 4.9 48.6 1.0

Magnesium binding site 6 out of 6 in 4naa

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Magnesium binding site 6 out of 6 in the Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Uvb Photoreceptor UVR8 From Arabidopsis Thaliana and Uv-Induced Structural Changes at 120K within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:47.4
occ:1.00
 O D:HOH800 2.0 51.9 1.0
O C:HOH880 2.0 58.6 1.0
O C:HOH726 2.1 49.5 1.0
O C:HOH881 2.2 43.5 1.0
O C:HOH803 2.3 43.5 1.0
O C:HOH836 4.0 51.8 1.0
O C:HOH738 4.0 39.4 1.0
O D:THR356 4.3 23.5 1.0
O C:HOH838 4.3 54.0 1.0
O C:HOH693 4.4 26.9 1.0
O C:HOH729 4.5 35.0 1.0
O C:HOH665 4.5 28.4 1.0
O C:HOH666 4.5 26.9 1.0

Reference:

X.Zeng, Z.Ren, Q.Wu, J.Fan, P.P.Peng, K.Tang, R.Zhang, K.H.Zhao, X.Yang. Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8. Nat Plants V. 1 2015.
ISSN: ISSN 2055-0278
PubMed: 26097745
DOI: 10.1038/NPLANTS.2014.6
Page generated: Mon Aug 19 23:26:48 2024

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