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

Protein crystallography data

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

Magnesium Binding Sites:

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 5z9x

Go back to Magnesium Binding Sites List in 5z9x
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 5z9x

Go back to Magnesium Binding Sites List in 5z9x
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

Reference:

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
Page generated: Mon Dec 14 22:16:42 2020

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