Sodium in PDB 6ktw: Structure of Eanb with Hercynine

The structure of Structure of Eanb with Hercynine, PDB code: 6ktw was solved by L.Wu, P.H.Liu, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.14 / 1.93
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.456, 112.038, 60.562, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 19.3

The structure of Structure of Eanb with Hercynine also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Structure of Eanb with Hercynine (pdb code 6ktw). 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 Eanb with Hercynine, PDB code: 6ktw:

Sodium binding site 1 out of 1 in the Structure of Eanb with Hercynine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Eanb with Hercynine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:42.4 occ:1.00 O A:SER332 2.6 31.6 1.0 O A:SER335 2.7 21.0 1.0 O A:MET329 3.1 23.0 1.0 OD1 A:ASP336 3.2 25.5 1.0 O A:HOH862 3.3 36.9 1.0 O A:LEU330 3.3 29.9 1.0 C A:LEU330 3.7 31.7 1.0 C A:SER332 3.7 36.6 1.0 C A:SER335 3.9 18.5 1.0 N A:SER332 4.0 27.7 1.0 CG A:ASP336 4.0 26.5 1.0 CA A:LEU330 4.1 20.2 1.0 C A:MET329 4.2 23.4 1.0 O A:HOH610 4.2 18.5 1.0 O A:HOH638 4.3 33.5 1.0 OD2 A:ASP336 4.4 24.8 1.0 N A:GLN331 4.4 29.3 1.0 CA A:SER332 4.5 25.9 1.0 CA A:ASP336 4.5 16.5 1.0 C A:GLN331 4.6 35.0 1.0 N A:LEU330 4.6 21.1 1.0 N A:ASP336 4.6 16.6 1.0 N A:GLU333 4.7 24.2 1.0 N A:SER335 4.8 21.6 1.0 CA A:SER335 4.9 20.5 1.0 CB A:ASP336 4.9 16.5 1.0 CA A:GLN331 4.9 31.7 1.0 CA A:GLU333 4.9 30.0 1.0

R.Cheng, L.Wu, R.Lai, C.Peng, N.Naowarojna, W.Hu, X.Li, S.A.Whelan, N.Lee, J.Lopez, C.Zhao, Y.Yong, J.Xue, X.Jiang, M.W.Grinstaff, Z.Deng, J.Chen, Q.Cui, J.H.Zhou, P.Liu. Single-Step Replacement of An Unreactive C-H Bond By A C-S Bond Using Polysulfide As the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis Acs Catalysis V. 10 8981 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C01809