Sodium in PDB 6ix9: The Structure of Lepi C52A in Complex with Sam and Leporin C

The structure of The Structure of Lepi C52A in Complex with Sam and Leporin C, PDB code: 6ix9 was solved by Y.Cai, M.Ohashi, Y.Hai, Y.Tang, J.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.96 / 1.78
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.348, 62.255, 113.874, 90.00, 113.49, 90.00
R / Rfree (%)	18.5 / 20.8

The structure of The Structure of Lepi C52A in Complex with Sam and Leporin C also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the The Structure of Lepi C52A in Complex with Sam and Leporin C (pdb code 6ix9). 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 Lepi C52A in Complex with Sam and Leporin C, PDB code: 6ix9:

Sodium binding site 1 out of 1 in the The Structure of Lepi C52A in Complex with Sam and Leporin C


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 Lepi C52A in Complex with Sam and Leporin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:22.0 occ:1.00 O B:HOH512 2.6 28.4 1.0 O B:ARG94 2.8 14.6 1.0 OD2 A:ASP339 3.0 25.1 1.0 O A:THR336 3.6 13.2 1.0 C B:ARG94 3.6 14.1 1.0 CG A:ASP339 3.7 27.3 1.0 CB A:ASP339 3.7 11.1 1.0 CA B:ARG94 3.8 14.8 1.0 CB A:THR336 3.8 15.2 1.0 N B:TYR98 3.9 13.1 1.0 CB B:ARG94 3.9 15.9 1.0 CB B:TYR98 4.0 14.2 1.0 CB B:ARG97 4.0 14.6 0.5 CA A:THR336 4.0 11.9 1.0 CD1 A:ILE340 4.1 21.5 1.0 CB B:ARG97 4.2 16.1 0.5 CG2 A:THR336 4.2 17.5 1.0 C A:THR336 4.2 11.4 1.0 CG1 A:ILE340 4.3 17.0 1.0 CA B:TYR98 4.4 13.4 1.0 C B:ARG97 4.6 14.5 1.0 O B:HOH683 4.7 26.5 1.0 CG B:ARG94 4.7 19.8 1.0 OD1 A:ASP339 4.7 23.9 1.0 NE B:ARG97 4.7 17.1 0.5 N A:ILE340 4.8 13.8 1.0 N B:LEU95 4.8 14.8 1.0 CA B:ARG97 4.9 15.8 0.5 CA B:ARG97 4.9 15.9 0.5 CD B:ARG97 4.9 17.3 0.5 CA A:ASP339 4.9 11.2 1.0

Y.Cai, Y.Hai, M.Ohashi, C.S.Jamieson, M.Garcia-Borras, K.N.Houk, J.Zhou, Y.Tang. Structural Basis For Stereoselective Dehydration and Hydrogen-Bonding Catalysis By the Sam-Dependent Pericyclase Lepi. Nat.Chem. V. 11 812 2019.
ISSN: ESSN 1755-4349
PubMed: 31332284
DOI: 10.1038/S41557-019-0294-X