Sodium in PDB 4j43: Pyld Holoenzyme

The structure of Pyld Holoenzyme, PDB code: 4j43 was solved by F.Quitterer, P.Beck, A.Bacher, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.980, 211.880, 77.620, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.1

The structure of Pyld Holoenzyme also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyld Holoenzyme (pdb code 4j43). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pyld Holoenzyme, PDB code: 4j43:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyld Holoenzyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyld Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:30.1 occ:1.00 O A:CYS206 2.3 39.4 1.0 O A:THR204 2.3 34.7 1.0 O A:PRO227 2.3 39.0 1.0 OE1 A:GLU202 2.3 38.7 1.0 O A:HOH1002 3.0 39.1 1.0 CD A:GLU202 3.2 38.3 1.0 OE2 A:GLU202 3.3 37.3 1.0 C A:CYS206 3.4 42.1 1.0 C A:THR204 3.4 36.2 1.0 N A:CYS206 3.4 40.1 1.0 C A:PRO227 3.5 40.7 1.0 N A:ALA229 3.8 42.1 1.0 C A:GLY225 3.9 37.5 1.0 CA A:CYS206 4.0 43.1 1.0 C A:CYS228 4.0 43.9 1.0 CA A:ALA229 4.0 40.6 1.0 N A:ILE226 4.1 39.7 1.0 CA A:GLY225 4.1 35.6 1.0 CG2 A:THR204 4.1 35.8 1.0 O A:GLY225 4.1 37.6 1.0 CA A:THR204 4.2 37.0 1.0 C A:PRO205 4.2 41.0 1.0 CB A:THR204 4.2 39.4 1.0 N A:PRO205 4.3 36.7 1.0 CB A:ALA229 4.3 38.7 1.0 N A:PRO227 4.4 43.5 1.0 N A:THR204 4.4 35.8 1.0 N A:CYS228 4.4 42.3 1.0 C A:ILE226 4.4 41.3 1.0 O A:CYS228 4.4 46.5 1.0 CA A:PRO205 4.4 39.2 1.0 CA A:CYS228 4.4 45.2 1.0 N A:ALA207 4.5 42.6 1.0 CA A:PRO227 4.6 42.2 1.0 CG A:GLU202 4.6 36.0 1.0 CA A:ILE226 4.6 41.9 1.0 OG1 A:THR209 4.7 44.7 1.0 OG1 A:THR223 4.8 39.0 1.0 O A:ILE226 4.8 40.9 1.0 CA A:ALA207 4.8 45.5 1.0

Sodium binding site 2 out of 2 in the Pyld Holoenzyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyld Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:25.9 occ:1.00 O B:CYS206 2.3 35.5 1.0 O B:THR204 2.3 31.1 1.0 O B:PRO227 2.3 35.9 1.0 OE1 B:GLU202 2.3 31.6 1.0 O B:HOH1057 3.1 38.8 1.0 CD B:GLU202 3.1 31.9 1.0 OE2 B:GLU202 3.2 34.1 1.0 C B:THR204 3.3 30.9 1.0 C B:CYS206 3.4 37.8 1.0 N B:CYS206 3.5 36.5 1.0 C B:PRO227 3.5 37.6 1.0 C B:GLY225 3.9 33.4 1.0 N B:ALA229 3.9 38.6 1.0 N B:ILE226 4.0 36.2 1.0 CA B:GLY225 4.0 31.6 1.0 CA B:CYS206 4.0 38.0 1.0 C B:CYS228 4.1 40.1 1.0 CB B:THR204 4.1 35.0 1.0 CA B:THR204 4.1 31.3 1.0 CA B:ALA229 4.1 36.9 1.0 CG2 B:THR204 4.1 33.7 1.0 N B:THR204 4.3 28.7 1.0 C B:PRO205 4.3 35.3 1.0 O B:GLY225 4.3 33.1 1.0 N B:PRO205 4.3 31.2 1.0 CB B:ALA229 4.4 35.9 1.0 N B:PRO227 4.4 40.9 1.0 C B:ILE226 4.4 38.4 1.0 N B:CYS228 4.4 38.7 1.0 N B:ALA207 4.5 39.3 1.0 CA B:CYS228 4.5 41.5 1.0 CA B:PRO205 4.5 33.0 1.0 O B:CYS228 4.5 40.6 1.0 CA B:PRO227 4.6 40.4 1.0 CG B:GLU202 4.6 31.4 1.0 CA B:ILE226 4.6 38.9 1.0 OG1 B:THR209 4.6 36.6 1.0 O B:ILE226 4.8 39.9 1.0 CA B:ALA207 4.8 40.8 1.0 OG1 B:THR223 4.9 38.1 1.0

F.Quitterer, P.Beck, A.Bacher, M.Groll. Structure and Reaction Mechanism of Pyrrolysine Synthase (Pyld). Angew.Chem.Int.Ed.Engl. V. 52 7033 2013.
ISSN: ISSN 1433-7851
PubMed: 23720358
DOI: 10.1002/ANIE.201301164