Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Pyld Holoenzyme (pdb code 4j43). 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, PDB code: 4j43:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyld Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyld Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:42.1 occ:1.00 O7N A:NAD901 2.6 29.6 1.0 OE2 A:GLU245 2.8 43.9 1.0 OH A:TYR129 3.0 28.4 1.0 O A:GLU245 3.0 34.5 1.0 N A:GLY250 3.1 29.3 1.0 N A:ILE249 3.4 30.1 1.0 C7N A:NAD901 3.4 29.8 1.0 N A:LEU247 3.4 33.6 1.0 N7N A:NAD901 3.5 30.5 1.0 C A:LEU247 3.5 30.7 1.0 CB A:ILE249 3.6 32.3 1.0 CE1 A:TYR129 3.6 26.7 1.0 CA A:LEU247 3.7 31.9 1.0 O A:LEU247 3.7 30.3 1.0 CA A:ILE249 3.7 31.0 1.0 CZ A:TYR129 3.8 27.4 1.0 C A:GLU245 3.9 37.2 1.0 N A:GLY248 3.9 30.5 1.0 C A:ILE249 3.9 29.8 1.0 C A:PRO246 4.0 36.6 1.0 CA A:GLY250 4.0 27.2 1.0 CD A:GLU245 4.0 42.0 1.0 O A:HOH1001 4.1 33.0 1.0 C A:GLY248 4.3 31.1 1.0 O A:PRO246 4.4 36.0 1.0 CG1 A:ILE249 4.5 32.8 1.0 CB A:GLU245 4.5 36.9 1.0 N A:PRO246 4.6 38.8 1.0 CA A:GLY248 4.6 31.8 1.0 CG2 A:ILE249 4.7 31.4 1.0 CA A:PRO246 4.7 39.6 1.0 CA A:GLU245 4.7 37.1 1.0 C3N A:NAD901 4.8 29.6 1.0 OE1 A:GLU245 4.8 44.1 1.0 CG A:GLU245 4.9 39.1 1.0 CD1 A:TYR129 4.9 28.0 1.0

Magnesium binding site 2 out of 2 in the Pyld Holoenzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyld Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:37.6 occ:1.00 O7N B:NAD901 2.2 30.8 1.0 O B:GLU245 2.9 40.3 1.0 OH B:TYR129 2.9 32.7 1.0 OE2 B:GLU245 3.0 48.7 1.0 C7N B:NAD901 3.1 29.2 1.0 N7N B:NAD901 3.3 30.4 1.0 N B:GLY250 3.3 28.9 1.0 N B:LEU247 3.4 33.5 1.0 C B:LEU247 3.5 29.2 1.0 N B:ILE249 3.5 31.1 1.0 CE1 B:TYR129 3.6 31.4 1.0 CA B:LEU247 3.6 30.4 1.0 O B:LEU247 3.7 29.6 1.0 CZ B:TYR129 3.7 31.8 1.0 CB B:ILE249 3.8 30.8 1.0 C B:GLU245 3.8 38.3 1.0 O B:HOH1031 3.9 30.7 1.0 N B:GLY248 3.9 28.5 1.0 C B:PRO246 3.9 34.0 1.0 CA B:ILE249 4.0 30.3 1.0 CD B:GLU245 4.1 45.5 1.0 C B:ILE249 4.1 29.0 1.0 CA B:GLY250 4.2 28.2 1.0 O B:PRO246 4.3 34.9 1.0 C B:GLY248 4.4 31.3 1.0 C3N B:NAD901 4.4 28.0 1.0 N B:PRO246 4.5 38.7 1.0 CB B:GLU245 4.6 40.4 1.0 CG1 B:ILE249 4.6 33.6 1.0 CA B:PRO246 4.7 36.2 1.0 CA B:GLY248 4.7 30.6 1.0 CA B:GLU245 4.7 38.2 1.0 OE1 B:GLU245 4.7 45.0 1.0 CG2 B:ILE249 4.9 30.1 1.0 CD1 B:TYR129 4.9 29.4 1.0 CG2 B:THR125 4.9 26.5 1.0 CG B:GLU245 5.0 44.4 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