Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyld Holoenzyme Soaked with L-Lysine-Ne-D-Ornithine, PDB code: 4j49:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg903 b:38.6 occ:1.00 O7N A:NAD901 2.6 29.4 1.0 OE1 A:GLU245 2.8 46.8 1.0 OH A:TYR129 2.8 31.1 1.0 O A:GLU245 3.0 39.5 1.0 N A:GLY250 3.2 27.6 1.0 C7N A:NAD901 3.4 29.6 1.0 N A:ILE249 3.4 29.3 1.0 N7N A:NAD901 3.4 29.7 1.0 N A:LEU247 3.5 30.3 1.0 CE1 A:TYR129 3.5 31.1 1.0 C A:LEU247 3.6 27.4 1.0 CB A:ILE249 3.6 30.3 1.0 CZ A:TYR129 3.6 31.4 1.0 CA A:LEU247 3.7 29.1 1.0 O A:LEU247 3.8 28.8 1.0 CA A:ILE249 3.8 28.9 1.0 C A:GLU245 3.8 39.0 1.0 N A:GLY248 3.9 26.5 1.0 CD A:GLU245 3.9 45.3 1.0 C A:ILE249 4.0 27.2 1.0 O A:HOH1001 4.0 26.8 1.0 C A:PRO246 4.0 32.2 1.0 CA A:GLY250 4.1 25.7 1.0 C A:GLY248 4.3 30.1 1.0 CG1 A:ILE249 4.4 32.2 1.0 CB A:GLU245 4.4 40.7 1.0 O A:PRO246 4.5 34.6 1.0 N A:PRO246 4.6 39.1 1.0 CA A:GLU245 4.6 39.7 1.0 CA A:GLY248 4.7 28.9 1.0 CG2 A:ILE249 4.7 30.8 1.0 OE2 A:GLU245 4.7 41.9 1.0 C3N A:NAD901 4.7 28.9 1.0 CA A:PRO246 4.7 36.7 1.0 CG A:GLU245 4.8 45.4 1.0 CD1 A:TYR129 4.9 28.8 1.0 CD1 A:ILE249 4.9 32.1 1.0 CE2 A:TYR129 5.0 30.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg904 b:36.1 occ:1.00 O7N B:NAI901 2.6 36.8 1.0 OE2 B:GLU245 2.8 44.5 1.0 OH B:TYR129 3.0 32.1 1.0 N B:GLY250 3.1 27.6 1.0 O B:GLU245 3.1 37.8 1.0 N B:ILE249 3.4 31.0 1.0 C7N B:NAI901 3.4 36.3 1.0 N B:LEU247 3.5 36.2 1.0 N7N B:NAI901 3.5 36.2 1.0 C B:LEU247 3.5 32.2 1.0 CB B:ILE249 3.6 31.4 1.0 CE1 B:TYR129 3.6 26.8 1.0 CA B:LEU247 3.7 33.9 1.0 O B:LEU247 3.7 31.0 1.0 CA B:ILE249 3.7 30.6 1.0 CZ B:TYR129 3.8 29.4 1.0 N B:GLY248 3.9 32.8 1.0 C B:GLU245 3.9 38.8 1.0 C B:ILE249 3.9 28.6 1.0 C B:PRO246 4.0 39.0 1.0 CD B:GLU245 4.0 43.4 1.0 CA B:GLY250 4.0 25.7 1.0 O B:HOH1001 4.1 35.2 1.0 C B:GLY248 4.2 30.9 1.0 O B:PRO246 4.4 39.0 1.0 CG1 B:ILE249 4.5 31.6 1.0 CB B:GLU245 4.5 38.5 1.0 N B:PRO246 4.5 40.0 1.0 CA B:GLY248 4.6 31.5 1.0 CG2 B:ILE249 4.6 31.7 1.0 CA B:PRO246 4.7 40.6 1.0 CA B:GLU245 4.7 38.8 1.0 OE1 B:GLU245 4.7 45.7 1.0 C3N B:NAI901 4.8 36.5 1.0 CG B:GLU245 4.9 39.3 1.0 CD1 B:TYR129 4.9 26.4 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