Magnesium in PDB 4q3a: Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+

The structure of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+, PDB code: 4q3a 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	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.490, 259.850, 48.660, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.4

The structure of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ (pdb code 4q3a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+, PDB code: 4q3a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine 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-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:30.1 occ:1.00 O7N A:NAI901 2.6 21.5 1.0 OE2 A:GLU245 2.6 27.3 1.0 OH A:TYR129 2.8 22.1 1.0 O A:GLU245 2.9 24.9 1.0 N A:GLY250 3.3 19.4 1.0 N A:LEU247 3.3 22.7 1.0 N7N A:NAI901 3.3 22.2 1.0 C7N A:NAI901 3.3 22.1 1.0 N A:ILE249 3.4 20.1 1.0 C A:LEU247 3.5 21.3 1.0 CE1 A:TYR129 3.6 21.8 1.0 CA A:LEU247 3.7 21.8 1.0 CB A:ILE249 3.7 20.2 1.0 CZ A:TYR129 3.7 22.1 1.0 C A:GLU245 3.7 25.0 1.0 N A:GLY248 3.8 20.9 1.0 CD A:GLU245 3.8 27.3 1.0 CA A:ILE249 3.9 19.9 1.0 O A:LEU247 3.9 21.0 1.0 C A:PRO246 3.9 23.7 1.0 O A:HOH1002 4.0 20.5 1.0 C A:ILE249 4.1 19.6 1.0 CA A:GLY250 4.2 19.1 1.0 C A:GLY248 4.3 20.4 1.0 N A:PRO246 4.4 24.9 1.0 O A:PRO246 4.5 24.2 1.0 OE1 A:GLU245 4.5 27.6 1.0 CA A:PRO246 4.5 24.3 1.0 CG1 A:ILE249 4.5 20.4 1.0 CB A:GLU245 4.5 26.3 1.0 CA A:GLY248 4.6 20.6 1.0 CA A:GLU245 4.6 25.6 1.0 CG2 A:ILE249 4.7 20.2 1.0 CG A:GLU245 4.8 26.8 1.0 C3N A:NAI901 4.8 22.1 1.0 CD1 A:TYR129 5.0 21.7 1.0

Magnesium binding site 2 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine 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-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:33.6 occ:1.00 O7N B:NAI901 2.7 23.4 1.0 OE2 B:GLU245 2.8 25.8 1.0 OH B:TYR129 2.9 23.1 1.0 N B:GLY250 3.1 19.6 1.0 O B:GLU245 3.1 22.6 1.0 N B:ILE249 3.3 20.0 1.0 C7N B:NAI901 3.5 24.1 1.0 N7N B:NAI901 3.5 23.7 1.0 CE1 B:TYR129 3.5 22.8 1.0 N B:LEU247 3.5 21.7 1.0 CB B:ILE249 3.5 19.9 1.0 C B:LEU247 3.6 20.8 1.0 CZ B:TYR129 3.6 23.2 1.0 CA B:ILE249 3.7 19.9 1.0 C B:ILE249 3.8 19.7 1.0 O B:LEU247 3.9 20.9 1.0 CA B:LEU247 3.9 21.1 1.0 N B:GLY248 3.9 20.7 1.0 C B:GLU245 3.9 23.6 1.0 CA B:GLY250 4.0 19.5 1.0 CD B:GLU245 4.0 25.6 1.0 O B:HOH1001 4.0 20.8 1.0 C B:PRO246 4.1 22.2 1.0 C B:GLY248 4.2 20.3 1.0 CG1 B:ILE249 4.4 20.1 1.0 CG2 B:ILE249 4.5 19.9 1.0 N B:PRO246 4.5 23.3 1.0 CA B:GLY248 4.6 20.7 1.0 OE1 B:GLU245 4.6 26.1 1.0 O B:PRO246 4.7 22.1 1.0 CB B:GLU245 4.7 25.1 1.0 CA B:PRO246 4.7 22.7 1.0 CD1 B:TYR129 4.8 22.7 1.0 CA B:GLU245 4.8 24.7 1.0 C3N B:NAI901 4.8 24.2 1.0 CD1 B:ILE249 4.9 20.2 1.0 CG B:GLU245 5.0 25.5 1.0 CE2 B:TYR129 5.0 23.4 1.0

Magnesium binding site 3 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg903 b:52.4 occ:1.00 OH C:TYR129 2.7 36.0 1.0 OE2 C:GLU245 2.8 51.0 1.0 O7N C:NAI901 2.8 40.2 1.0 O C:GLU245 2.9 41.0 1.0 N C:GLY250 3.2 35.8 1.0 N C:ILE249 3.4 38.0 1.0 N C:LEU247 3.4 40.9 1.0 N7N C:NAI901 3.5 40.4 1.0 CE1 C:TYR129 3.5 36.0 1.0 C7N C:NAI901 3.5 40.2 1.0 CZ C:TYR129 3.6 36.6 1.0 CB C:ILE249 3.6 37.8 1.0 C C:LEU247 3.6 39.3 1.0 C C:GLU245 3.7 42.7 1.0 CA C:ILE249 3.8 36.9 1.0 CA C:LEU247 3.8 39.5 1.0 O C:LEU247 3.9 39.1 1.0 CD C:GLU245 3.9 49.4 1.0 C C:PRO246 3.9 41.5 1.0 N C:GLY248 4.0 39.2 1.0 C C:ILE249 4.0 36.4 1.0 O C:HOH1002 4.1 33.5 1.0 CA C:GLY250 4.1 35.5 1.0 C C:GLY248 4.3 38.4 1.0 N C:PRO246 4.4 43.0 1.0 CG1 C:ILE249 4.5 38.8 1.0 O C:PRO246 4.5 41.5 1.0 CA C:PRO246 4.5 42.5 1.0 CB C:GLU245 4.5 46.8 1.0 OE1 C:GLU245 4.6 49.1 1.0 CG2 C:ILE249 4.6 37.8 1.0 CA C:GLU245 4.6 44.6 1.0 CA C:GLY248 4.7 39.6 1.0 CD1 C:TYR129 4.8 35.9 1.0 CG C:GLU245 4.9 48.3 1.0 CE2 C:TYR129 4.9 37.2 1.0 C3N C:NAI901 4.9 39.3 1.0 CD1 C:ILE249 4.9 39.2 1.0 N C:GLU245 5.0 43.8 1.0

Magnesium binding site 4 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg903 b:63.9 occ:1.00 OE2 D:GLU245 2.7 59.6 1.0 O D:GLU245 2.7 50.8 1.0 O7N D:NAI901 2.8 46.0 1.0 OH D:TYR129 2.9 49.8 1.0 N D:ILE249 3.3 53.9 1.0 N D:LEU247 3.3 50.6 1.0 N D:GLY250 3.3 50.8 1.0 N7N D:NAI901 3.4 45.2 1.0 C D:LEU247 3.5 50.0 1.0 C7N D:NAI901 3.5 44.1 1.0 CE1 D:TYR129 3.7 49.3 1.0 C D:GLU245 3.7 52.7 1.0 CB D:ILE249 3.7 55.9 1.0 CA D:LEU247 3.7 50.0 1.0 CZ D:TYR129 3.7 49.8 1.0 O D:LEU247 3.7 49.0 1.0 N D:GLY248 3.8 51.6 1.0 CA D:ILE249 3.8 54.7 1.0 C D:PRO246 3.9 50.9 1.0 CD D:GLU245 3.9 59.3 1.0 C D:ILE249 4.0 52.9 1.0 O D:HOH1004 4.1 38.6 1.0 C D:GLY248 4.2 54.1 1.0 CA D:GLY250 4.3 49.5 1.0 CG1 D:ILE249 4.3 57.0 1.0 N D:PRO246 4.3 53.3 1.0 CA D:GLY248 4.5 52.9 1.0 CA D:PRO246 4.5 52.2 1.0 O D:PRO246 4.5 50.0 1.0 CB D:GLU245 4.5 56.2 1.0 CA D:GLU245 4.6 54.6 1.0 OE1 D:GLU245 4.6 59.7 1.0 CG D:GLU245 4.8 58.3 1.0 CG2 D:ILE249 4.9 57.2 1.0 C3N D:NAI901 4.9 42.3 1.0 CD1 D:ILE249 4.9 57.7 1.0 CD1 D:TYR129 5.0 49.2 1.0 N D:GLU245 5.0 53.4 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