Magnesium in PDB 5z9x: Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate

The structure of Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate, PDB code: 5z9x was solved by J.Chen, L.Liu, C.You, J.Gu, W.Ruan, L.Zhang, J.Gan, C.Cao, Y.Huang, X.Chen, J.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.99 / 2.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.993, 87.993, 178.639, 90.00, 90.00, 120.00
R / Rfree (%)	25.2 / 26.1

The binding sites of Magnesium atom in the Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate (pdb code 5z9x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate, PDB code: 5z9x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:81.6 occ:0.97 OD2 A:ASP144 2.2 0.7 1.0 O A:HIS223 2.9 79.3 1.0 CG A:ASP144 3.3 0.0 1.0 OD2 A:ASP228 3.3 94.4 1.0 OP1 R:G10 3.3 0.6 1.0 OD1 A:ASP144 3.7 0.8 1.0 O3' R:A9 3.8 99.5 1.0 C A:HIS223 4.0 72.1 1.0 P R:G10 4.1 97.1 1.0 OD1 A:ASP228 4.1 92.5 1.0 CG A:ASP228 4.1 84.1 1.0 CB A:HIS223 4.3 80.6 1.0 N A:HIS223 4.3 99.4 1.0 CA A:HIS223 4.4 79.4 1.0 CB A:ASP144 4.5 73.0 1.0 C4' R:A9 4.5 95.8 1.0 OP2 R:G10 4.7 78.7 1.0 MG A:MG503 4.7 0.2 0.6 C3' R:A9 4.7 89.0 1.0 C5' R:A9 4.7 0.4 1.0 OD2 A:ASP283 4.9 0.1 1.0 CA A:ASP144 4.9 66.4 1.0

Magnesium binding site 2 out of 2 in the Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Arabidopsis Small Rna Degrading Nuclease 1 in Complex with An Rna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:0.2 occ:0.57 OD1 A:ASP144 2.1 0.8 1.0 OD2 A:ASP283 2.2 0.1 1.0 OE2 A:GLU146 2.2 0.6 0.4 OP1 R:G10 2.2 0.6 1.0 O A:CYS145 3.0 69.3 1.0 CG A:ASP283 3.1 0.0 1.0 P R:G10 3.3 97.1 1.0 CG A:ASP144 3.3 0.0 1.0 CD A:GLU146 3.3 0.1 0.4 CA A:CYS280 3.6 96.1 1.0 O5' R:G10 3.7 80.1 1.0 CB A:ASP283 3.7 0.2 1.0 C5' R:G10 3.8 89.9 1.0 OP2 R:G10 3.8 78.7 1.0 CB A:CYS280 3.9 86.0 1.0 OD2 A:ASP144 3.9 0.7 1.0 C A:CYS145 4.0 73.2 1.0 N A:CYS280 4.0 0.8 1.0 CG A:GLU146 4.1 0.9 0.6 OD1 A:ASP283 4.1 0.7 1.0 OE1 A:GLU146 4.1 1.0 0.4 CG A:GLU146 4.2 0.2 0.4 C A:ASP279 4.4 96.9 1.0 CB A:ASP144 4.4 73.0 1.0 CB A:HIS278 4.5 0.1 1.0 N A:CYS145 4.6 64.8 1.0 O3' R:A9 4.6 99.5 1.0 O A:ASP279 4.7 97.2 1.0 MG A:MG502 4.7 81.6 1.0 N A:GLU146 4.7 84.0 1.0 CA A:CYS145 4.8 65.6 1.0 N A:ASP279 4.9 0.4 1.0 C A:CYS280 4.9 97.6 1.0 CD A:GLU146 4.9 0.6 0.6 OE2 A:GLU146 4.9 0.9 0.6 ND1 A:HIS278 4.9 0.9 1.0 CA A:GLU146 4.9 89.6 0.4 CA A:GLU146 5.0 86.6 0.6

J.Chen, L.Liu, C.You, J.Gu, W.Ruan, L.Zhang, J.Gan, C.Cao, Y.Huang, X.Chen, J.Ma. Structural and Biochemical Insights Into Small Rna 3' End Trimming By Arabidopsis SDN1. Nat Commun V. 9 3585 2018.
ISSN: ESSN 2041-1723
PubMed: 30181559
DOI: 10.1038/S41467-018-05942-7