Sodium in PDB 6a47: Structure of TREX2 in Complex with A Y Structured Dsdna

All present enzymatic activity of Structure of TREX2 in Complex with A Y Structured Dsdna:
3.1.11.2;

The structure of Structure of TREX2 in Complex with A Y Structured Dsdna, PDB code: 6a47 was solved by Y.Y.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.45 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.666, 48.404, 90.593, 90.00, 97.36, 90.00
R / Rfree (%)	16.3 / 19.1

The structure of Structure of TREX2 in Complex with A Y Structured Dsdna also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Structure of TREX2 in Complex with A Y Structured Dsdna (pdb code 6a47). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of TREX2 in Complex with A Y Structured Dsdna, PDB code: 6a47:

Sodium binding site 1 out of 1 in the Structure of TREX2 in Complex with A Y Structured Dsdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of TREX2 in Complex with A Y Structured Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:44.3 occ:1.00 H A:GLU191 2.0 31.3 1.0 OG A:SER189 2.4 51.0 1.0 HB2 A:GLU191 2.7 35.5 1.0 N A:GLU191 2.9 26.1 1.0 HB3 A:GLU191 3.0 35.5 1.0 OE2 A:GLU29 3.0 29.8 1.0 H A:ALA190 3.1 37.2 1.0 CB A:GLU191 3.2 29.6 1.0 N A:ALA190 3.3 31.0 1.0 CD A:GLU29 3.5 28.1 1.0 HB3 A:ALA190 3.5 28.4 1.0 O A:HOH449 3.5 42.7 1.0 HG21 A:THR61 3.6 29.4 1.0 CA A:GLU191 3.6 26.2 1.0 CB A:SER189 3.6 48.2 1.0 HH12 B:ARG55 3.7 31.4 1.0 OE1 A:GLU29 3.7 28.1 1.0 H A:GLY192 3.7 29.5 1.0 C A:SER189 3.8 39.9 1.0 O B:HOH450 3.8 32.9 1.0 C A:ALA190 3.9 27.8 1.0 HA A:SER189 4.0 60.5 1.0 HB3 A:SER189 4.0 57.9 1.0 CA A:ALA190 4.0 28.9 1.0 CA A:SER189 4.0 50.4 1.0 O A:HOH490 4.1 43.1 1.0 NH1 B:ARG55 4.2 26.1 1.0 CB A:ALA190 4.2 23.6 1.0 HG23 A:THR61 4.2 29.4 1.0 HB2 A:SER189 4.3 57.9 1.0 HA A:GLU191 4.3 31.4 1.0 CG2 A:THR61 4.3 24.5 1.0 N A:GLY192 4.4 24.6 1.0 HH22 B:ARG55 4.5 34.1 1.0 CG A:GLU191 4.5 33.8 1.0 HH11 B:ARG55 4.5 31.4 1.0 HB2 A:SER31 4.5 32.6 1.0 HG2 A:GLU29 4.5 32.5 1.0 O A:SER189 4.6 36.3 1.0 C A:GLU191 4.6 26.2 1.0 OE1 A:GLU191 4.6 33.4 1.0 CG A:GLU29 4.6 27.1 1.0 O B:HOH421 4.6 57.6 1.0 HB2 A:ALA190 4.7 28.4 1.0 HG1 A:THR61 4.7 30.9 1.0 CD A:GLU191 4.8 37.6 1.0 HG22 A:THR61 4.8 29.4 1.0 HG3 A:GLU29 4.9 32.5 1.0 CZ B:ARG55 4.9 30.5 1.0 HA A:ALA190 4.9 34.6 1.0 NH2 B:ARG55 4.9 28.4 1.0 HB1 A:ALA190 5.0 28.4 1.0

H.L.Cheng, C.T.Lin, K.W.Huang, S.Wang, Y.T.Lin, S.I.Toh, Y.Y.Hsiao. Structural Insights Into the Duplex Dna Processing of TREX2 Nucleic Acids Res. V. 46 12166 2018.
ISSN: ESSN 1362-4962
PubMed: 30357414
DOI: 10.1093/NAR/GKY970