Sodium in PDB 6ix8: The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue

The structure of The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue, PDB code: 6ix8 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)	28.80 / 1.66
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.800, 62.562, 113.836, 90.00, 113.34, 90.00
R / Rfree (%)	16.8 / 19.7

The structure of The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue (pdb code 6ix8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue, PDB code: 6ix8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue


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 Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:30.7 occ:1.00 O B:HOH795 2.4 34.1 1.0 O B:HOH647 2.5 16.2 1.0 O A:HOH662 2.6 37.8 1.0 O A:ALA331 3.1 11.2 1.0 CA A:GLY330 3.5 7.8 1.0 C A:GLY330 3.6 7.3 1.0 CA B:SER101 3.7 9.3 0.6 CA B:SER101 3.8 9.1 0.5 OG B:SER101 3.8 5.8 0.5 N B:SER101 3.8 6.6 1.0 N A:ALA331 3.8 6.5 1.0 C B:ALA100 3.9 7.5 1.0 O B:ALA100 4.0 7.8 1.0 CB B:ALA100 4.1 6.3 1.0 O A:GLY330 4.1 9.3 1.0 CB B:SER101 4.1 9.1 0.6 C A:ALA331 4.1 7.0 1.0 N A:GLY330 4.3 9.5 1.0 O B:HOH752 4.3 37.0 1.0 O B:HOH730 4.3 39.0 1.0 OE1 B:GLN107 4.3 10.4 1.0 CB B:SER101 4.3 9.4 0.5 O B:HOH630 4.4 17.6 1.0 O A:HOH749 4.6 33.7 1.0 CA A:ALA331 4.6 6.6 1.0 CA B:ALA100 4.7 6.8 1.0 O B:ARG97 4.7 8.8 1.0 CL A:CL403 4.8 17.9 1.0 CD B:GLN107 4.9 10.9 1.0

Sodium binding site 2 out of 3 in the The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:36.1 occ:1.00 O A:HOH847 2.3 31.2 1.0 O A:HOH775 2.9 22.7 1.0 CB A:GLU328 3.8 13.2 1.0 CE A:LYS329 3.9 26.4 1.0 O A:HOH727 4.2 16.9 1.0 O B:HOH742 4.2 37.2 1.0 O A:HOH687 4.3 30.1 1.0 CD A:LYS329 4.3 23.4 1.0 CG A:LYS329 4.3 12.6 1.0 CG A:GLU328 4.4 19.7 1.0 CA A:GLU328 5.0 11.4 1.0 N A:LYS329 5.0 8.6 1.0 NZ A:LYS329 5.0 30.5 1.0

Sodium binding site 3 out of 3 in the The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Lepi C52A in Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:28.8 occ:1.00 OD1 B:ASP110 2.4 43.1 1.0 O B:HOH813 2.8 34.5 1.0 O B:HOH788 2.8 22.5 1.0 OG1 B:THR108 3.0 15.0 1.0 CG B:ASP110 3.1 40.5 1.0 OD2 B:ASP110 3.2 45.5 1.0 CB B:THR108 3.4 12.9 1.0 CG B:PRO75 3.6 14.7 1.0 CB B:PRO75 3.6 15.1 1.0 CG2 B:THR108 3.6 13.7 1.0 CB B:LYS112 4.1 17.2 1.0 CD B:LYS112 4.1 21.9 1.0 CG B:LYS112 4.5 16.2 1.0 CB B:ASP110 4.6 27.7 1.0 N B:ASP110 4.8 16.0 1.0 CD B:PRO75 4.8 14.6 1.0 CE B:LYS112 4.9 25.0 1.0 CA B:THR108 4.9 12.5 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