Sodium in PDB 4j49: Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine

The structure of Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine, PDB code: 4j49 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 (°)	81.280, 211.450, 77.260, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.5

The structure of Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine (pdb code 4j49). 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 Soaked with L-Lysine-Ne-D-Ornithine, PDB code: 4j49:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:36.7 occ:1.00 O A:HOH1002 2.4 39.0 1.0 O A:CYS206 2.5 40.0 1.0 O A:THR204 2.5 30.2 1.0 O A:PRO227 2.6 46.5 1.0 OE1 A:GLU202 2.8 31.9 1.0 OE2 A:GLU202 3.2 30.7 1.0 CD A:GLU202 3.4 30.8 1.0 C A:THR204 3.5 31.1 1.0 C A:CYS206 3.6 41.4 1.0 N A:CYS206 3.6 38.7 1.0 N A:ALA229 3.7 46.1 1.0 C A:PRO227 3.8 51.4 1.0 C A:GLY225 3.9 41.0 1.0 CA A:GLY225 4.0 38.3 1.0 CA A:ALA229 4.0 43.5 1.0 C A:CYS228 4.1 49.3 1.0 N A:ILE226 4.1 46.2 1.0 CG2 A:THR204 4.1 32.5 1.0 CB A:THR204 4.2 33.7 1.0 CA A:CYS206 4.2 40.7 1.0 CA A:THR204 4.2 30.0 1.0 O A:GLY225 4.3 38.6 1.0 CB A:ALA229 4.3 40.2 1.0 N A:THR204 4.3 27.7 1.0 C A:PRO205 4.4 37.4 1.0 N A:PRO205 4.5 31.7 1.0 O A:CYS228 4.5 48.6 1.0 CA A:CYS228 4.5 52.8 1.0 C A:ILE226 4.6 52.4 1.0 CA A:PRO205 4.6 33.8 1.0 N A:PRO227 4.6 51.8 1.0 N A:CYS228 4.6 52.1 1.0 N A:ALA207 4.6 43.1 1.0 OG1 A:THR223 4.6 35.1 1.0 CA A:ILE226 4.7 53.2 1.0 OG1 A:THR209 4.7 34.1 1.0 CG A:GLU202 4.8 29.3 1.0 CA A:PRO227 4.8 51.8 1.0 O A:ILE226 4.9 52.1 1.0 CA A:ALA207 5.0 45.1 1.0

Sodium binding site 2 out of 2 in the Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:41.5 occ:1.00 O B:HOH1005 2.4 39.4 1.0 O B:THR204 2.5 35.0 1.0 O B:CYS206 2.5 52.2 1.0 O B:PRO227 2.7 52.3 1.0 OE1 B:GLU202 2.8 43.3 1.0 OE2 B:GLU202 3.3 45.2 1.0 CD B:GLU202 3.4 44.2 1.0 C B:THR204 3.5 40.6 1.0 C B:CYS206 3.5 51.3 1.0 N B:CYS206 3.6 46.1 1.0 N B:ALA229 3.7 49.6 1.0 C B:PRO227 3.9 55.2 1.0 C B:GLY225 3.9 48.3 1.0 CA B:ALA229 4.0 45.9 1.0 CA B:GLY225 4.1 45.5 1.0 C B:CYS228 4.1 51.9 1.0 CA B:CYS206 4.1 49.6 1.0 O B:GLY225 4.2 44.5 1.0 CB B:THR204 4.2 45.6 1.0 N B:ILE226 4.2 54.2 1.0 CA B:THR204 4.2 42.3 1.0 CB B:ALA229 4.2 42.8 1.0 C B:PRO205 4.3 46.9 1.0 CG2 B:THR204 4.3 45.1 1.0 N B:PRO205 4.4 42.4 1.0 N B:THR204 4.4 38.5 1.0 CA B:PRO205 4.5 44.9 1.0 N B:ALA207 4.5 50.6 1.0 CA B:CYS228 4.5 53.0 1.0 OG1 B:THR223 4.6 39.6 1.0 O B:CYS228 4.6 54.5 1.0 OG1 B:THR209 4.7 43.3 1.0 N B:CYS228 4.7 53.3 1.0 C B:ILE226 4.7 61.3 1.0 N B:PRO227 4.7 61.3 1.0 CA B:ILE226 4.9 60.9 1.0 CA B:ALA207 4.9 52.7 1.0 CG B:GLU202 4.9 42.6 1.0 CA B:PRO227 4.9 58.2 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