Sodium in PDB 7exx: The Structure of Dndg

The structure of The Structure of Dndg, PDB code: 7exx was solved by D.Wu, L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.02 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	139.248, 182.286, 59.492, 90, 90, 90
R / Rfree (%)	16.6 / 21.4

The binding sites of Sodium atom in the The Structure of Dndg (pdb code 7exx). 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 The Structure of Dndg, PDB code: 7exx:

Sodium binding site 1 out of 1 in the The Structure of Dndg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Dndg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:26.2 occ:1.00 O A:ARG427 2.3 26.9 1.0 O A:ASP430 2.3 24.0 1.0 C A:ARG427 3.5 25.8 1.0 C A:ASP430 3.5 25.9 1.0 CA A:SER431 4.0 27.5 1.0 CA A:MET428 4.2 26.0 1.0 N A:SER431 4.2 25.8 1.0 N A:MET428 4.3 25.5 1.0 N A:GLY432 4.4 30.2 1.0 C A:MET428 4.4 26.5 1.0 CA A:ARG427 4.5 26.4 1.0 N A:ASP430 4.5 27.1 1.0 CA A:ASP430 4.7 27.8 1.0 C A:SER431 4.8 28.1 1.0 O A:MET428 4.8 26.9 1.0 N A:SER429 4.9 26.8 1.0

D.Wu, Y.Tang, S.Chen, Y.He, X.Chang, W.Zheng, Z.Deng, Z.Li, L.Wang, G.Wu, S.Chen. The Functional Coupling Between Restriction and Dna Phosphorothioate Modification Systems Underlying the Dndfgh Restriction Complex Nat Catal 2022.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00884-2