Sodium in PDB 4qz9: Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair

All present enzymatic activity of Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair:
2.7.7.31;

The structure of Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair, PDB code: 4qz9 was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.06 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.936, 74.720, 126.357, 90.00, 100.06, 90.00
R / Rfree (%)	18.4 / 20.4

The structure of Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair (pdb code 4qz9). 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 Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair, PDB code: 4qz9:

Sodium binding site 1 out of 1 in the Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:42.9 occ:1.00 O A:VAL258 2.3 37.7 1.0 O A:HOH847 2.4 46.6 1.0 O A:VAL255 2.4 39.3 1.0 O A:THR253 2.4 43.1 1.0 OP1 U:DA5 2.6 51.5 1.0 O U:HOH102 2.7 48.8 1.0 C A:VAL258 3.3 39.8 1.0 C A:THR253 3.4 43.1 1.0 C A:VAL255 3.5 40.0 1.0 N A:VAL258 3.5 37.0 1.0 P U:DA5 3.8 53.6 1.0 CA A:THR253 3.8 39.2 1.0 CA A:VAL258 3.9 37.2 1.0 OP2 U:DA5 4.0 54.1 1.0 N A:GLY257 4.1 34.6 1.0 CA A:PHE256 4.1 34.8 1.0 N A:VAL255 4.2 39.1 1.0 N A:PHE256 4.2 36.4 1.0 CB A:THR253 4.2 38.9 1.0 CB A:VAL258 4.3 40.1 1.0 O U:HOH103 4.3 58.6 1.0 N A:GLY259 4.4 39.3 1.0 C A:PHE256 4.4 37.4 1.0 N A:SER254 4.5 39.4 1.0 CA A:VAL255 4.5 38.6 1.0 C A:SER254 4.5 43.7 1.0 C A:GLY257 4.6 38.7 1.0 O3' U:DA4 4.7 53.7 1.0 CA A:GLY259 4.7 39.2 1.0 CA A:SER254 4.9 38.8 1.0 O A:PHE252 4.9 42.6 1.0 CA A:GLY257 4.9 34.6 1.0 O5' U:DA5 5.0 56.0 1.0

J.Gouge, S.Rosario, F.Romain, F.Poitevin, P.Beguin, M.Delarue. Structural Basis For A Novel Mechanism of Dna Bridging and Alignment in Eukaryotic Dsb Dna Repair. Embo J. V. 34 1126 2015.
ISSN: ISSN 0261-4189
PubMed: 25762590
DOI: 10.15252/EMBJ.201489643