Sodium in PDB 8c4n: Cdaa-Amp Complex

All present enzymatic activity of Cdaa-Amp Complex:
2.7.7.85;

The structure of Cdaa-Amp Complex, PDB code: 8c4n was solved by P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.85 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.61, 64.72, 129.92, 90, 90, 90
R / Rfree (%)	22.2 / 25.5

The structure of Cdaa-Amp Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Cdaa-Amp Complex (pdb code 8c4n). 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 Cdaa-Amp Complex, PDB code: 8c4n:

Sodium binding site 1 out of 1 in the Cdaa-Amp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cdaa-Amp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:71.6 occ:1.00 O B:ASN51 2.5 50.3 1.0 O A:ASN51 2.7 49.1 1.0 O B:HOH323 2.9 66.8 1.0 OE2 A:GLU80 3.3 72.5 1.0 CE A:LYS53 3.6 69.2 1.0 C B:ASN51 3.6 49.3 1.0 CB B:ASN51 3.7 45.5 1.0 O B:HOH326 3.8 61.6 1.0 C A:ASN51 3.8 46.3 1.0 OE2 B:GLU80 3.8 68.8 1.0 CD A:GLU80 4.2 66.7 1.0 CA B:ASN51 4.3 45.2 1.0 NZ A:LYS53 4.4 72.3 1.0 CA A:ALA52 4.4 44.6 1.0 O B:LEU50 4.5 49.2 1.0 N A:ALA52 4.5 41.1 1.0 CD B:GLU80 4.6 63.2 1.0 C A:ALA52 4.7 40.4 1.0 N B:ALA52 4.7 45.1 1.0 N A:LYS53 4.7 39.7 1.0 CB A:ASN51 4.8 49.8 1.0 CD A:LYS53 4.8 69.0 1.0 CG A:GLU80 4.9 57.9 1.0 CA A:ASN51 4.9 48.7 1.0 CG B:ASN51 5.0 56.0 1.0 CA B:ALA52 5.0 46.9 1.0

P.Neumann, P.Kloskowski, R.Ficner. Computer-Aided Design of A Cyclic Di-Amp Synthesizing Enzyme Cdaa Inhibitor. Microlife V. 4 AD021 2023.
ISSN: ISSN 2633-6693
PubMed: 37223749
DOI: 10.1093/FEMSML/UQAD021