Sodium in PDB 6eom: Structure of Dpp III From Caldithrix Abyssi

The structure of Structure of Dpp III From Caldithrix Abyssi, PDB code: 6eom was solved by I.Sabljic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.472, 90.549, 132.973, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24

The structure of Structure of Dpp III From Caldithrix Abyssi also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Structure of Dpp III From Caldithrix Abyssi (pdb code 6eom). 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 Structure of Dpp III From Caldithrix Abyssi, PDB code: 6eom:

Sodium binding site 1 out of 1 in the Structure of Dpp III From Caldithrix Abyssi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Dpp III From Caldithrix Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:41.5 occ:1.00 O A:ALA313 2.3 34.0 1.0 O A:VAL315 2.4 32.6 1.0 O A:HOH949 2.4 51.2 1.0 O A:THR311 2.4 30.9 1.0 C A:THR311 3.2 30.8 1.0 C A:ALA313 3.5 33.5 1.0 C A:VAL315 3.6 33.0 1.0 O A:ASP310 3.6 30.3 1.0 CA A:THR311 3.8 30.1 1.0 NZ A:LYS606 3.8 43.5 1.0 N A:ALA313 3.8 31.9 1.0 N A:VAL315 4.1 33.6 1.0 C A:LYS312 4.1 31.4 1.0 CA A:ALA313 4.2 31.1 1.0 N A:LYS312 4.2 30.6 1.0 C A:GLY314 4.4 33.5 1.0 CA A:VAL315 4.5 33.7 1.0 N A:GLN316 4.5 31.1 1.0 CA A:GLN316 4.5 29.6 1.0 N A:GLY314 4.5 33.8 1.0 CA A:LYS312 4.5 30.7 1.0 C A:ASP310 4.6 31.2 1.0 O A:LYS312 4.7 31.8 1.0 OG1 A:THR311 4.7 27.4 1.0 CB A:ALA313 4.7 30.7 1.0 N A:THR311 4.7 30.2 1.0 O A:HOH808 4.7 30.8 1.0 OG1 A:THR317 4.8 35.6 1.0 CA A:GLY314 4.8 33.5 1.0 O A:GLY314 4.8 34.0 1.0 CB A:THR311 4.9 27.8 1.0 NE2 A:GLN316 4.9 33.0 1.0 C A:GLN316 5.0 29.8 1.0 CE A:LYS606 5.0 43.2 1.0

I.Sabljic, M.Tomin, M.Matovina, I.Sucec, A.Tomasic Paic, A.Tomic, M.Abramic, S.Tomic. The First Dipeptidyl Peptidase III From A Thermophile: Structural Basis For Thermal Stability and Reduced Activity. Plos One V. 13 92488 2018.
ISSN: ESSN 1932-6203
PubMed: 29420664
DOI: 10.1371/JOURNAL.PONE.0192488