Sodium in PDB 5ywv: Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna

All present enzymatic activity of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna:
3.1.11.2;

The structure of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna, PDB code: 5ywv 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)	29.31 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.192, 80.713, 85.247, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 22

The structure of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna (pdb code 5ywv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna, PDB code: 5ywv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:20.3 occ:1.00 N A:ALA214 3.4 26.2 1.0 N A:GLN213 3.4 21.4 1.0 C A:LYS211 3.6 22.1 1.0 CB A:GLN213 3.6 29.5 1.0 CB A:LYS211 3.6 31.5 1.0 CA A:LYS211 3.7 25.4 1.0 CG A:GLN213 3.8 37.5 1.0 N A:PRO212 3.8 21.3 1.0 O A:LYS211 3.9 22.5 1.0 CA A:GLN213 3.9 24.2 1.0 CD A:PRO212 4.0 19.3 1.0 CB A:ALA214 4.0 19.6 1.0 C A:GLN213 4.1 26.8 1.0 CA A:ALA214 4.3 25.1 1.0 C A:PRO212 4.4 23.5 1.0 CG A:LYS211 4.7 30.3 1.0 CA A:PRO212 4.7 20.0 1.0 CG A:PRO212 4.7 21.2 1.0 CD A:LYS211 4.8 36.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:42.5 occ:1.00 N B:LEU24 3.0 28.0 1.0 O D:HOH205 3.4 45.5 1.0 CA B:GLY23 3.5 20.5 1.0 N2 D:DG7 3.7 33.6 1.0 OG B:SER27 3.7 27.0 1.0 CB B:SER27 3.7 25.4 1.0 C B:GLY23 3.7 24.7 1.0 OG B:SER78 4.0 24.1 1.0 CA B:LEU24 4.1 26.9 1.0 O B:LEU24 4.1 29.6 1.0 CB B:LEU24 4.1 27.6 1.0 CB B:SER78 4.2 27.1 1.0 C2 D:DG7 4.3 33.4 1.0 N3 D:DG7 4.4 33.3 1.0 CG B:LEU24 4.5 29.8 1.0 C B:LEU24 4.5 28.8 1.0 N B:GLY23 4.8 25.9 1.0 CD1 B:LEU24 4.8 30.8 1.0 O B:THR22 4.9 23.9 1.0 O B:GLY23 5.0 24.2 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:30.0 occ:1.00 N B:GLN213 3.3 34.3 1.0 C B:LYS211 3.4 34.2 1.0 CB B:GLN213 3.4 45.7 1.0 CA B:LYS211 3.4 33.7 1.0 N B:ALA214 3.5 37.4 1.0 CB B:LYS211 3.6 31.8 1.0 N B:PRO212 3.6 33.9 1.0 CD B:PRO212 3.7 35.8 1.0 CA B:GLN213 3.8 39.1 1.0 O B:LYS211 3.8 34.0 1.0 C B:GLN213 4.2 37.6 1.0 CB B:ALA214 4.2 35.6 1.0 C B:PRO212 4.2 30.4 1.0 CG B:LYS211 4.3 33.2 1.0 CA B:ALA214 4.5 37.1 1.0 CA B:PRO212 4.5 31.8 1.0 CG B:GLN213 4.7 56.4 1.0 N B:LYS211 4.9 32.2 1.0 NE2 B:GLN213 4.9 65.6 1.0 CD B:LYS211 4.9 34.9 1.0 CG B:PRO212 5.0 34.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:45.9 occ:1.00 N B:SER26 2.9 36.2 1.0 OG B:SER26 3.3 45.2 1.0 CB B:SER26 3.4 41.1 1.0 N B:PRO25 3.5 28.8 1.0 CD B:PRO25 3.5 29.6 1.0 CB B:LEU24 3.7 27.6 1.0 CA B:SER26 3.8 38.2 1.0 C B:LEU24 3.8 28.8 1.0 C B:PRO25 3.9 38.6 1.0 CB B:PRO25 3.9 28.7 1.0 CA B:PRO25 4.0 31.5 1.0 CG B:PRO25 4.1 29.6 1.0 O B:LEU24 4.2 29.6 1.0 CA B:LEU24 4.4 26.9 1.0 N1 D:DI6 4.5 44.6 1.0 C B:SER26 4.9 36.3 1.0 CG B:LEU24 4.9 29.8 1.0 N B:SER27 5.0 34.7 1.0 C2 D:DI6 5.0 44.3 1.0

K.W.Huang, T.C.Liu, R.Y.Liang, L.Y.Chu, H.L.Cheng, J.W.Chu, Y.Y.Hsiao. Structural Basis For Overhang Excision and Terminal Unwinding of Dna Duplexes By TREX1 Plos Biol. V. 16 05653 2018.
ISSN: ESSN 1545-7885
PubMed: 29734329
DOI: 10.1371/JOURNAL.PBIO.2005653