Sodium in PDB 6s16: T. Thermophilus Ruvc in Complex with Holliday Junction Substrate

All present enzymatic activity of T. Thermophilus Ruvc in Complex with Holliday Junction Substrate:
3.1.22.4;

The structure of T. Thermophilus Ruvc in Complex with Holliday Junction Substrate, PDB code: 6s16 was solved by K.M.Gorecka, M.Krepl, A.Szlachcic, J.Poznanski, J.Sponer, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.30 / 3.41
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.066, 108.066, 133.281, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 23.1

The structure of T. Thermophilus Ruvc in Complex with Holliday Junction Substrate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the T. Thermophilus Ruvc in Complex with Holliday Junction Substrate (pdb code 6s16). 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 T. Thermophilus Ruvc in Complex with Holliday Junction Substrate, PDB code: 6s16:

Sodium binding site 1 out of 1 in the T. Thermophilus Ruvc in Complex with Holliday Junction Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of T. Thermophilus Ruvc in Complex with Holliday Junction Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:87.5 occ:1.00 CB B:PRO43 3.4 0.6 1.0 O A:LEU166 3.4 98.4 1.0 N A:VAL102 3.6 94.2 1.0 O A:VAL102 3.7 89.9 1.0 CD B:LYS45 3.8 90.8 1.0 CB A:PRO101 3.9 0.7 1.0 CA A:PRO101 4.0 95.3 1.0 CG B:PRO43 4.1 0.7 1.0 CB A:PRO165 4.1 0.2 1.0 C A:PRO101 4.2 97.5 1.0 CG B:LYS45 4.3 91.4 1.0 C A:LEU166 4.4 0.4 1.0 N A:LEU166 4.4 0.3 1.0 C A:VAL102 4.5 91.8 1.0 CA B:PRO43 4.5 1.0 1.0 CA A:VAL102 4.5 94.9 1.0 CA A:PRO165 4.9 0.9 1.0 NZ B:LYS45 4.9 93.4 1.0 CB A:VAL102 5.0 95.2 1.0

K.M.Gorecka, M.Krepl, A.Szlachcic, J.Poznanski, J.Sponer, M.Nowotny. Ruvc Uses Dynamic Probing of the Holliday Junction to Achieve Sequence Specificity and Efficient Resolution. Nat Commun V. 10 4102 2019.
ISSN: ESSN 2041-1723
PubMed: 31506434
DOI: 10.1038/S41467-019-11900-8