Sodium in PDB 6ghs: Modification Dependent Tagi Restriction Endonuclease

The structure of Modification Dependent Tagi Restriction Endonuclease, PDB code: 6ghs was solved by M.Kisiala, A.Copelas, H.Czapinska, S.Xu, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.92
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.963, 72.963, 207.576, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.3

The structure of Modification Dependent Tagi Restriction Endonuclease also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Modification Dependent Tagi Restriction Endonuclease (pdb code 6ghs). 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 Modification Dependent Tagi Restriction Endonuclease, PDB code: 6ghs:

Sodium binding site 1 out of 1 in the Modification Dependent Tagi Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Modification Dependent Tagi Restriction Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:45.8 occ:1.00 O A:HOH516 2.0 46.0 1.0 O A:HOH519 2.2 46.6 1.0 OD2 A:ASP258 2.7 32.2 1.0 O A:HOH545 2.9 41.1 1.0 NE2 A:HIS254 3.2 26.6 1.0 CG A:ASP258 3.5 31.2 1.0 OD1 A:ASP258 3.5 33.3 1.0 O A:HOH551 3.8 25.1 1.0 CE1 A:HIS254 4.1 27.0 1.0 CD2 A:HIS254 4.1 26.7 1.0 N A:HIS229 4.1 38.2 1.0 O A:HIS229 4.2 35.2 1.0 CA A:ALA228 4.5 39.3 1.0 C A:ALA228 4.7 38.9 1.0 CB A:ALA228 4.8 39.2 1.0 CB A:HIS229 4.8 39.5 1.0 CA A:HIS229 4.9 37.9 1.0 CB A:ASP258 4.9 30.3 1.0 C A:HIS229 5.0 36.2 1.0

M.Kisiala, A.Copelas, H.Czapinska, S.Y.Xu, M.Bochtler. Crystal Structure of the Modification-Dependent Sra-Hnh Endonuclease Tagi. Nucleic Acids Res. V. 46 10489 2018.
ISSN: ESSN 1362-4962
PubMed: 30202937
DOI: 10.1093/NAR/GKY781