Sodium in PDB 6lzx: Structure of Phytolacca Americana UGT3 with 15-Crown-5

The structure of Structure of Phytolacca Americana UGT3 with 15-Crown-5, PDB code: 6lzx was solved by R.Maharjan, Y.Fukuda, T.Nakayama, T.Nakayama, H.Hamada, S.Ozaki, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.73 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.173, 103.298, 110.383, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26

The structure of Structure of Phytolacca Americana UGT3 with 15-Crown-5 also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Sodium atom in the Structure of Phytolacca Americana UGT3 with 15-Crown-5 (pdb code 6lzx). 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 Phytolacca Americana UGT3 with 15-Crown-5, PDB code: 6lzx:

Sodium binding site 1 out of 1 in the Structure of Phytolacca Americana UGT3 with 15-Crown-5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Phytolacca Americana UGT3 with 15-Crown-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:35.6 occ:1.00 O A:GLU238 1.9 74.8 1.0 O1 A:EYO501 2.0 46.2 1.0 O2 A:EYO501 2.5 52.0 1.0 O B:GLU238 2.6 45.9 1.0 O5 A:EYO501 2.6 56.0 1.0 O4 A:EYO501 2.7 50.4 1.0 O3 A:EYO501 2.9 57.4 1.0 C9 A:EYO501 3.0 52.0 1.0 C1 A:EYO501 3.0 48.7 1.0 C A:GLU238 3.1 63.4 1.0 C10 A:EYO501 3.1 55.7 1.0 C2 A:EYO501 3.2 50.4 1.0 C3 A:EYO501 3.3 54.1 1.0 C4 A:EYO501 3.3 55.6 1.0 C7 A:EYO501 3.3 50.1 1.0 C8 A:EYO501 3.4 52.9 1.0 C6 A:EYO501 3.6 54.7 1.0 C5 A:EYO501 3.7 57.6 1.0 C B:GLU238 3.8 45.6 1.0 CA A:LEU239 3.9 56.2 1.0 N A:LEU239 3.9 61.7 1.0 CA A:GLU238 4.1 64.0 1.0 CD2 A:LEU239 4.4 63.5 1.0 CA B:GLU238 4.5 46.1 1.0 CB A:GLU238 4.6 70.8 1.0 C A:LEU239 4.6 51.8 1.0 N B:LEU239 4.7 48.5 1.0 O B:LYS237 4.8 47.0 1.0 CA B:LEU239 4.8 48.9 1.0 O A:LYS237 5.0 58.7 1.0

R.Maharjan, Y.Fukuda, T.Nakayama, T.Nakayama, H.Hamada, S.Ozaki, T.Inoue. Crown-Ether-Mediated Crystal Structures of the Glycosyltransferase PAGT3 From Phytolacca Americana. Acta Crystallogr.,Sect.D 2020.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798320005306