Magnesium in PDB 4q3e: Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+

The structure of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+, PDB code: 4q3e 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 (°)	79.080, 210.460, 77.640, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.5

The structure of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ (pdb code 4q3e). 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 Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+, PDB code: 4q3e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:41.3 occ:1.00 O7N A:NAD901 2.6 33.6 1.0 OH A:TYR129 2.8 36.0 1.0 OE2 A:GLU245 2.9 43.5 1.0 O A:GLU245 2.9 36.1 1.0 N A:GLY250 3.3 32.1 1.0 C7N A:NAD901 3.4 34.2 1.0 N A:ILE249 3.4 32.5 1.0 N7N A:NAD901 3.4 34.4 1.0 N A:LEU247 3.5 36.7 1.0 CE1 A:TYR129 3.6 35.1 1.0 CB A:ILE249 3.6 35.6 1.0 C A:LEU247 3.6 32.6 1.0 CZ A:TYR129 3.7 35.3 1.0 CA A:LEU247 3.8 34.7 1.0 C A:GLU245 3.8 37.9 1.0 CA A:ILE249 3.8 33.5 1.0 O A:LEU247 3.8 31.7 1.0 N A:GLY248 3.9 33.2 1.0 CD A:GLU245 4.0 42.0 1.0 O A:HOH1001 4.0 32.4 1.0 C A:PRO246 4.0 37.5 1.0 C A:ILE249 4.0 33.6 1.0 CA A:GLY250 4.2 30.6 1.0 C A:GLY248 4.3 32.2 1.0 CG1 A:ILE249 4.3 36.2 1.0 O A:PRO246 4.5 37.5 1.0 CB A:GLU245 4.5 40.3 1.0 N A:PRO246 4.5 38.8 1.0 OE1 A:GLU245 4.6 42.8 1.0 CA A:GLU245 4.6 39.3 1.0 CA A:GLY248 4.6 32.5 1.0 CG2 A:ILE249 4.7 36.7 1.0 CA A:PRO246 4.7 38.3 1.0 C3N A:NAD901 4.7 33.7 1.0 CD1 A:TYR129 4.9 34.0 1.0 CG A:GLU245 4.9 41.3 1.0 CD1 A:ILE249 5.0 36.8 1.0 N A:GLU245 5.0 39.7 1.0 CE2 A:TYR129 5.0 35.7 1.0

Magnesium binding site 2 out of 2 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:46.3 occ:1.00 O7N B:NAD901 2.7 38.2 1.0 OE2 B:GLU245 2.9 48.0 1.0 O B:GLU245 3.0 40.9 1.0 OH B:TYR129 3.0 33.5 1.0 N B:GLY250 3.1 33.1 1.0 N B:ILE249 3.4 34.5 1.0 C7N B:NAD901 3.4 38.0 1.0 N B:LEU247 3.5 39.6 1.0 C B:LEU247 3.5 37.4 1.0 CE1 B:TYR129 3.5 34.2 1.0 N7N B:NAD901 3.5 37.3 1.0 CB B:ILE249 3.6 35.2 1.0 CA B:LEU247 3.7 39.0 1.0 CZ B:TYR129 3.7 34.4 1.0 O B:LEU247 3.7 34.5 1.0 CA B:ILE249 3.8 35.0 1.0 C B:ILE249 3.9 34.2 1.0 N B:GLY248 3.9 37.1 1.0 C B:GLU245 3.9 42.7 1.0 CA B:GLY250 4.0 33.1 1.0 O B:HOH1003 4.0 32.5 1.0 CD B:GLU245 4.0 46.7 1.0 C B:PRO246 4.0 40.8 1.0 C B:GLY248 4.3 35.6 1.0 CG1 B:ILE249 4.5 35.9 1.0 O B:PRO246 4.5 39.9 1.0 CA B:GLY248 4.6 36.6 1.0 CB B:GLU245 4.6 44.4 1.0 CG2 B:ILE249 4.7 35.4 1.0 N B:PRO246 4.7 42.5 1.0 OE1 B:GLU245 4.7 47.2 1.0 CA B:GLU245 4.8 43.6 1.0 C3N B:NAD901 4.8 37.7 1.0 CA B:PRO246 4.8 43.1 1.0 CD1 B:TYR129 4.8 34.5 1.0 CG B:GLU245 5.0 45.7 1.0 CG2 B:THR125 5.0 30.7 1.0

F.Quitterer, P.Beck, A.Bacher, M.Groll. The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed By Pyrrolysine Synthase (Pyld). Angew.Chem.Int.Ed.Engl. V. 53 8150 2014.
ISSN: ISSN 1433-7851
PubMed: 24916332
DOI: 10.1002/ANIE.201402595