Sodium in PDB 6vyd: Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation

The structure of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation, PDB code: 6vyd was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.17 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.599, 87.260, 163.209, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.4

The structure of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation (pdb code 6vyd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation, PDB code: 6vyd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:17.7 occ:1.00 O A:THR225 2.3 16.2 1.0 OE1 A:GLU98 2.4 16.3 1.0 O A:HOH721 2.4 20.4 1.0 O A:HOH678 2.5 17.9 1.0 OG A:SER224 2.5 19.4 1.0 O A:HOH674 2.6 14.9 1.0 C A:THR225 3.3 17.4 1.0 CB A:SER224 3.5 19.0 1.0 CD A:GLU98 3.6 14.6 1.0 O A:HOH557 3.8 14.7 1.0 C A:SER224 4.0 16.3 1.0 N A:THR225 4.0 16.7 1.0 CB A:GLU98 4.1 16.6 1.0 N A:LEU226 4.1 16.4 1.0 CA A:LEU226 4.2 15.9 1.0 O A:SER224 4.2 19.3 1.0 O A:HOH729 4.2 20.7 1.0 CA A:THR225 4.3 15.6 1.0 CG A:GLU98 4.3 14.8 1.0 CA A:SER224 4.4 17.8 1.0 CG A:GLU217 4.5 16.0 1.0 N A:ILE227 4.5 14.1 1.0 CB A:GLU217 4.6 15.1 1.0 OE2 A:GLU98 4.6 14.8 1.0 CD A:GLU217 4.8 15.5 1.0 O A:HOH581 4.8 14.1 1.0 O A:HOH587 4.9 21.2 1.0 C A:LEU226 4.9 15.7 1.0

Sodium binding site 2 out of 2 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:36.4 occ:1.00 O B:HOH667 2.3 32.2 1.0 O B:THR225 2.3 33.8 1.0 OE1 B:GLU98 2.4 30.8 1.0 OG B:SER224 2.5 34.6 1.0 O B:HOH618 2.5 26.4 1.0 O B:HOH612 2.5 30.9 1.0 C B:THR225 3.3 33.1 1.0 CD B:GLU98 3.6 29.0 1.0 CB B:SER224 3.6 33.1 1.0 C B:SER224 3.9 36.3 1.0 O B:HOH566 3.9 20.3 1.0 N B:THR225 4.0 36.2 1.0 CA B:LEU226 4.0 31.7 1.0 N B:LEU226 4.0 33.5 1.0 O B:SER224 4.0 37.1 1.0 CB B:GLU98 4.1 30.2 1.0 CA B:THR225 4.2 35.4 1.0 CG B:GLU98 4.3 30.6 1.0 N B:ILE227 4.3 30.4 1.0 CA B:SER224 4.3 33.6 1.0 O B:HOH669 4.4 33.9 1.0 OE2 B:GLU98 4.5 23.4 1.0 CG B:GLU217 4.6 26.5 1.0 CB B:GLU217 4.6 27.7 1.0 C B:LEU226 4.7 32.5 1.0 O B:HOH558 4.7 22.3 1.0 CD B:GLU217 4.8 26.4 1.0 CB B:THR225 4.9 36.1 1.0 O B:HOH554 5.0 29.9 1.0

C.J.Herbst-Gervasoni, D.W.Christianson. Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation To Be Published.