Sodium in PDB 7d78: The Structure of Thioesterase Dcsb

The structure of The Structure of Thioesterase Dcsb, PDB code: 7d78 was solved by Y.Tang, J.H.Zhou, G.Q.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.84 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.707, 47.569, 71.695, 90, 93.19, 90
R / Rfree (%)	14.6 / 18.3

The structure of The Structure of Thioesterase Dcsb also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the The Structure of Thioesterase Dcsb (pdb code 7d78). 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 Thioesterase Dcsb, PDB code: 7d78:

Sodium binding site 1 out of 1 in the The Structure of Thioesterase Dcsb


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 Thioesterase Dcsb within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:29.5 occ:1.00 O D:GLU146 2.8 26.0 1.0 N D:LYS150 3.0 21.0 1.0 O D:HOH728 3.0 34.8 1.0 O D:HOH624 3.1 23.7 1.0 CG D:LYS150 3.2 32.7 1.0 N D:ASP149 3.4 20.4 1.0 C D:LYS147 3.4 24.8 1.0 CB D:LYS150 3.5 23.2 1.0 O D:LYS147 3.6 20.8 1.0 O D:HOH520 3.7 42.0 1.0 CA D:LYS147 3.7 25.3 1.0 C D:GLU146 3.7 26.4 1.0 CA D:LYS150 3.8 17.1 1.0 C D:ASP149 3.8 21.4 1.0 CA D:ASP149 3.9 23.2 1.0 N D:ARG148 3.9 23.2 1.0 CB D:ASP149 3.9 23.1 1.0 CD D:LYS150 4.1 43.1 1.0 N D:LYS147 4.1 22.7 1.0 C D:ARG148 4.1 23.8 1.0 CE D:LYS150 4.6 44.9 1.0 CA D:ARG148 4.6 21.4 1.0 O D:HOH711 4.7 33.0 1.0 CG D:ASP149 4.9 26.4 1.0 O D:ARG148 4.9 21.2 1.0 C D:LYS150 5.0 21.4 1.0 CA D:GLU146 5.0 25.6 1.0 O D:ASP149 5.0 21.8 1.0

D.W.Gao, C.S.Jamieson, G.Wang, Y.Yan, J.Zhou, K.N.Houk, Y.Tang. A Polyketide Cyclase That Forms Medium-Ring Lactones. J.Am.Chem.Soc. V. 143 80 2021.
ISSN: ESSN 1520-5126
PubMed: 33351624
DOI: 10.1021/JACS.0C11226