Magnesium in PDB 4nbm: Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K

The structure of Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K, PDB code: 4nbm was solved by X.Yang, X.Zeng, K.-H.Zhao, Z.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.86 / 1.61
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.310, 76.828, 191.253, 90.00, 96.75, 90.00
R / Rfree (%)	15 / 18.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K (pdb code 4nbm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 23 binding sites of Magnesium where determined in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K, PDB code: 4nbm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


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 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:38.0 occ:1.00 O B:HOH841 2.0 37.0 1.0 O A:HOH779 2.2 35.2 1.0 O B:HOH511 2.4 37.9 1.0 O B:HOH840 2.4 51.3 1.0 O B:HOH537 2.5 48.3 1.0 O A:HOH706 3.7 38.9 1.0 O A:HOH587 4.0 23.0 1.0 O A:HOH585 4.1 25.0 1.0 O A:HOH586 4.3 29.3 1.0 O A:HOH885 4.3 43.7 1.0 O B:HOH744 4.6 34.7 1.0 O B:THR356 4.6 18.4 1.0 OD2 A:ASP54 5.0 21.2 1.0 O A:HOH824 5.0 48.4 1.0

Magnesium binding site 2 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


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 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:32.9 occ:1.00 O A:HOH900 1.9 40.7 1.0 O A:HOH756 2.1 34.9 1.0 O A:HOH755 2.1 48.2 1.0 O A:HOH754 2.1 41.5 1.0 O B:HOH744 2.2 34.7 1.0 O B:HOH810 4.0 38.8 1.0 O A:HOH757 4.1 51.5 1.0 O B:HOH743 4.3 24.4 1.0 O A:HOH779 4.4 35.2 1.0 O B:HOH685 4.4 23.8 1.0 O A:THR356 4.5 18.3 1.0 O B:HOH684 4.7 27.4 1.0

Magnesium binding site 3 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


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 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:34.0 occ:1.00 O A:HOH905 2.0 38.4 1.0 O A:HOH847 2.1 38.3 1.0 O C:HOH859 2.2 36.9 1.0 O A:HOH906 2.2 41.8 1.0 O C:HOH888 2.3 42.8 1.0 O A:HOH907 2.4 52.6 1.0 OD1 A:ASP263 3.8 45.4 1.0 OE1 C:GLU262 4.0 47.3 1.0 O B:HOH625 4.2 35.9 1.0 O A:HOH762 4.2 42.7 1.0 OD2 A:ASP263 4.2 42.4 1.0 O A:HOH939 4.3 52.9 1.0 CG A:ASP263 4.4 43.7 1.0 O A:HOH875 4.6 40.3 1.0 CD C:GLU262 4.7 50.1 1.0 O C:HOH620 4.7 34.0 1.0 CG C:GLU262 4.7 37.4 1.0 O B:HOH512 4.9 42.7 1.0 O A:HOH614 4.9 36.8 1.0

Magnesium binding site 4 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


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 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:39.7 occ:1.00 O C:HOH699 1.9 27.5 1.0 O A:HOH903 2.2 35.2 1.0 O A:HOH908 2.3 39.3 1.0 O C:HOH700 2.3 32.8 1.0 O A:HOH874 2.5 50.0 1.0 O C:HOH886 2.6 42.3 1.0 O C:HOH840 4.1 29.8 1.0 O C:ARG200 4.2 20.6 1.0 O A:HOH902 4.3 38.2 1.0 OE1 A:GLU262 4.3 39.5 1.0 O D:HOH529 4.4 10.5 1.0 OE2 A:GLU262 4.7 43.6 1.0 CD C:ARG209 4.7 22.6 1.0 O C:HOH560 4.8 24.7 1.0 O D:HOH539 4.8 42.5 1.0 CD A:GLU262 5.0 43.2 1.0

Magnesium binding site 5 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


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 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:34.3 occ:1.00 O A:HOH935 2.0 46.3 1.0 O A:HOH909 2.0 36.8 1.0 O D:HOH881 2.1 33.5 1.0 O D:HOH882 2.2 39.0 1.0 NE2 A:HIS268 2.3 25.4 1.0 CE1 A:HIS268 3.1 29.3 1.0 CD2 A:HIS268 3.4 22.1 1.0 O A:HOH785 3.8 37.5 1.0 O A:HOH638 3.8 28.1 1.0 OE1 D:GLU158 4.1 40.0 1.0 O A:HOH639 4.2 18.5 1.0 ND1 A:HIS268 4.3 23.8 1.0 OE2 D:GLU158 4.3 36.6 1.0 O A:HOH637 4.4 23.4 1.0 CG A:HIS268 4.5 19.7 1.0 CD D:GLU158 4.6 40.8 1.0 O A:HOH828 4.9 50.9 1.0

Magnesium binding site 6 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


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 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:51.6 occ:1.00 O A:HOH807 2.0 48.2 1.0 OD2 A:ASP156 2.1 34.0 1.0 O A:HOH928 2.2 51.1 1.0 O A:HOH624 2.2 35.6 1.0 O A:HOH844 2.4 49.2 1.0 O A:HOH673 2.7 33.4 1.0 CG A:ASP156 3.2 31.2 1.0 OD1 A:ASP156 3.6 25.8 1.0 O A:HOH765 4.0 44.6 1.0 OE1 A:GLN164 4.3 28.6 1.0 CB A:ASP156 4.5 23.3 1.0 NE2 A:GLN164 4.7 29.9 1.0 CD A:GLN164 4.9 27.5 1.0 OE2 A:GLU158 4.9 63.7 1.0 CB A:LEU154 5.0 15.9 1.0

Magnesium binding site 7 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:19.5 occ:1.00 O A:HOH931 2.1 19.1 1.0 O A:GLY50 2.1 20.4 1.0 O A:HOH775 2.1 20.7 1.0 O B:HOH740 2.1 18.5 1.0 O B:HOH739 2.2 17.1 1.0 C A:GLY50 3.3 20.4 1.0 NZ B:LYS304 3.9 31.0 1.0 CA A:ASP51 3.9 18.9 1.0 N A:ASP51 4.1 22.8 1.0 O B:HOH807 4.2 26.1 1.0 O B:HOH741 4.3 30.3 1.0 O A:HOH932 4.4 29.4 1.0 CA A:GLY50 4.4 15.1 1.0 CB A:PHE109 4.7 15.6 1.0 C A:ASP51 4.8 17.4 1.0 CB A:ASP51 4.9 19.6 1.0 CG A:PHE109 4.9 16.6 1.0

Magnesium binding site 8 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:64.3 occ:1.00 O B:HOH719 2.1 37.5 1.0 O B:HOH534 2.1 46.9 1.0 O B:HOH852 2.5 36.6 1.0 O B:HOH855 2.7 44.1 1.0 O B:HOH533 2.9 47.0 1.0 O B:HOH880 3.2 49.0 1.0 OG B:SER71 3.8 33.5 1.0 O B:HOH635 3.9 29.1 1.0 O B:VAL72 3.9 22.8 1.0 OG1 B:THR73 4.0 31.5 1.0 O B:HOH889 4.4 52.3 1.0 CG2 B:ILE19 4.5 25.8 1.0 O B:HOH718 4.6 40.6 1.0 O B:HOH765 4.7 39.4 1.0 CD1 B:ILE19 4.9 36.9 1.0 C B:VAL72 4.9 21.5 1.0 O B:HOH720 4.9 28.5 1.0

Magnesium binding site 9 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:57.3 occ:1.00 O B:HOH814 2.3 35.9 1.0 O A:HOH937 2.5 56.3 1.0 O B:HOH844 2.5 34.4 1.0 O A:HOH823 2.8 34.3 1.0 O A:HOH675 3.9 33.6 1.0 O B:HOH687 4.0 38.7 1.0 O B:HOH688 4.0 32.4 1.0 O A:HOH671 4.0 29.3 1.0 O B:HOH561 4.2 25.2 1.0 O A:HOH503 4.4 26.3 1.0 O B:HOH691 4.4 42.0 1.0 OD2 B:ASP77 4.7 30.0 1.0 O A:HOH670 4.9 41.9 1.0 NH2 B:ARG41 4.9 19.6 1.0 CZ B:ARG41 4.9 22.1 1.0 O A:HOH667 5.0 37.2 1.0

Magnesium binding site 10 out of 23 in the Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Uvb Photoreceptor UVR8 and Light-Induced Structural Changes at 180K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:60.0 occ:1.00 O B:HOH553 2.0 47.8 1.0 O B:HOH554 2.2 41.5 1.0 O B:HOH555 2.3 43.0 1.0 O B:HOH556 2.3 44.6 1.0 O B:HOH557 2.3 41.5 1.0 O B:HOH897 2.3 48.9 1.0 O B:ASP327 4.2 27.1 1.0 O B:HOH558 4.3 47.6 1.0 OE2 B:GLU345 4.3 31.2 1.0 O B:HOH801 4.6 42.1 1.0 O B:ASP326 4.7 32.5 1.0 CE B:LYS329 4.8 34.2 1.0 O B:HOH525 4.8 45.8 1.0

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.
PubMed: 26097745
DOI: 10.1038/NPLANTS.2014.6