Sodium in PDB 7d48: Apo-Form Cyclic Trinucleotide Synthase Cdnd

The structure of Apo-Form Cyclic Trinucleotide Synthase Cdnd, PDB code: 7d48 was solved by C.-S.Yang, M.-H.Hou, C.-L.Tsai, Y.-C.Wang, T.-P.Ko, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.01 / 2.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	52.924, 52.924, 344.361, 90, 90, 90
R / Rfree (%)	18.2 / 22.8

The binding sites of Sodium atom in the Apo-Form Cyclic Trinucleotide Synthase Cdnd (pdb code 7d48). 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 Apo-Form Cyclic Trinucleotide Synthase Cdnd, PDB code: 7d48:

Sodium binding site 1 out of 1 in the Apo-Form Cyclic Trinucleotide Synthase Cdnd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo-Form Cyclic Trinucleotide Synthase Cdnd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na400 b:30.9 occ:1.00 O A:LEU260 2.5 15.4 1.0 O A:HOH569 2.5 23.0 1.0 O A:HOH550 2.5 21.6 1.0 O A:HOH752 2.5 37.0 1.0 O A:ASN258 2.5 24.0 1.0 O A:HOH757 2.6 36.4 1.0 C A:LEU260 3.4 22.9 1.0 C A:ASN258 3.5 19.7 1.0 NZ A:LYS217 3.5 27.8 1.0 O A:GLY257 3.8 17.8 1.0 N A:LEU260 3.9 20.6 1.0 C A:ALA259 4.0 21.2 1.0 N A:ASP261 4.2 23.7 1.0 O A:ALA259 4.2 17.1 1.0 CA A:ASN258 4.2 14.2 1.0 CA A:ASP261 4.3 22.0 1.0 CA A:LEU260 4.3 19.6 1.0 NH1 A:ARG281 4.3 22.0 1.0 N A:ALA259 4.4 18.8 1.0 OD1 A:ASP261 4.4 29.2 1.0 O A:HOH785 4.4 43.4 1.0 NH2 A:ARG281 4.6 24.4 1.0 CA A:ALA259 4.6 16.6 1.0 O A:HOH828 4.6 23.5 1.0 CE A:LYS217 4.6 26.0 1.0 C A:GLY257 4.8 18.5 1.0 O A:HOH630 4.9 43.3 1.0 CZ A:ARG281 5.0 24.9 1.0

C.-S.Yang, M.-H.Hou, C.-L.Tsai, Y.-C.Wang, T.-P.Ko, Y.Chen. Crystal Structure and Functional Implication of A Bacterial Cyclic Amp-Amp-Gmp Synthetase Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962