Magnesium in PDB 4j4b: Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh

The structure of Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh, PDB code: 4j4b 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)	10.00 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.383, 142.440, 167.305, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24

The structure of Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh (pdb code 4j4b). 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 in Complex with L-Lysine-Ne-D-Ornithine and Nadh, PDB code: 4j4b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:38.2 occ:1.00 O7N A:NAI901 2.2 37.1 1.0 O A:GLU245 2.9 39.6 1.0 OH A:TYR129 3.0 37.3 1.0 C7N A:NAI901 3.0 38.4 1.0 OE2 A:GLU245 3.2 42.3 1.0 N A:GLY250 3.2 35.8 1.0 N7N A:NAI901 3.2 37.9 1.0 CE2 A:TYR129 3.5 35.3 1.0 N A:LEU247 3.5 35.8 1.0 C A:LEU247 3.6 35.9 1.0 N A:ILE249 3.6 36.8 1.0 CZ A:TYR129 3.7 36.2 1.0 O A:LEU247 3.7 34.0 1.0 CB A:ILE249 3.7 36.7 1.0 CA A:LEU247 3.8 35.6 1.0 C A:GLU245 3.9 40.0 1.0 O A:HOH1003 3.9 31.2 1.0 C A:PRO246 4.0 36.7 1.0 CA A:ILE249 4.0 37.2 1.0 CA A:GLY250 4.0 33.4 1.0 C A:ILE249 4.1 36.9 1.0 N A:GLY248 4.1 36.7 1.0 CD A:GLU245 4.2 41.8 1.0 O A:PRO246 4.4 35.2 1.0 C3N A:NAI901 4.4 38.5 1.0 C A:GLY248 4.5 36.7 1.0 CG1 A:ILE249 4.5 35.7 1.0 N A:PRO246 4.6 40.0 1.0 CG2 A:THR125 4.6 35.4 1.0 CA A:PRO246 4.7 38.3 1.0 CD2 A:TYR129 4.8 34.9 1.0 CG2 A:ILE249 4.8 37.7 1.0 CB A:GLU245 4.8 43.7 1.0 CA A:GLY248 4.8 36.8 1.0 OE1 A:GLU245 4.9 41.3 1.0 CA A:GLU245 4.9 42.0 1.0

Magnesium binding site 2 out of 2 in the Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:20.1 occ:1.00 O7N B:NAI302 2.2 14.9 1.0 OE2 B:GLU245 2.9 12.8 1.0 OH B:TYR129 3.0 14.9 1.0 N B:GLY250 3.1 9.2 1.0 C7N B:NAI302 3.2 15.9 1.0 O B:GLU245 3.3 14.4 1.0 N B:ILE249 3.4 9.4 1.0 N7N B:NAI302 3.5 15.1 1.0 C B:LEU247 3.5 10.6 1.0 CE2 B:TYR129 3.5 14.1 1.0 N B:LEU247 3.6 11.7 1.0 O B:LEU247 3.7 10.2 1.0 CB B:ILE249 3.7 9.4 1.0 CZ B:TYR129 3.8 14.4 1.0 CA B:LEU247 3.8 11.3 1.0 N B:GLY248 3.8 10.2 1.0 CA B:ILE249 3.8 9.4 1.0 O B:HOH402 3.8 13.2 1.0 C B:ILE249 3.9 9.2 1.0 CA B:GLY250 3.9 9.3 1.0 CD B:GLU245 4.0 13.5 1.0 C B:PRO246 4.0 12.6 1.0 C B:GLU245 4.1 14.5 1.0 C B:GLY248 4.3 9.6 1.0 CG1 B:ILE249 4.5 9.8 1.0 O B:PRO246 4.5 12.8 1.0 C3N B:NAI302 4.5 17.4 1.0 CA B:GLY248 4.6 9.9 1.0 OE1 B:GLU245 4.6 13.4 1.0 N B:PRO246 4.7 14.1 1.0 CA B:PRO246 4.7 13.6 1.0 CD2 B:TYR129 4.8 13.3 1.0 CB B:GLU245 4.8 15.0 1.0 CG2 B:ILE249 4.8 9.6 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