Magnesium in PDB 4q3b: Pyld Cocrystallized with L-Lysine-Ne-D-Lysine and Nad+

The structure of Pyld Cocrystallized with L-Lysine-Ne-D-Lysine and Nad+, PDB code: 4q3b 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	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.640, 261.170, 48.740, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.2

The structure of Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+ (pdb code 4q3b). 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-D-Lysine and Nad+, PDB code: 4q3b:
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-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-Lysine-Ne-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:25.5 occ:1.00 O7N A:NAI901 2.6 19.5 1.0 OE1 A:GLU245 2.8 22.3 1.0 OH A:TYR129 2.9 17.1 1.0 N A:GLY250 3.1 16.2 1.0 O A:GLU245 3.2 20.2 1.0 N A:ILE249 3.3 16.6 1.0 C7N A:NAI901 3.4 19.9 1.0 N7N A:NAI901 3.4 19.7 1.0 N A:LEU247 3.4 18.8 1.0 C A:LEU247 3.5 17.8 1.0 CE1 A:TYR129 3.5 16.9 1.0 CB A:ILE249 3.6 16.4 1.0 CZ A:TYR129 3.7 17.0 1.0 CA A:LEU247 3.7 18.1 1.0 N A:GLY248 3.7 17.4 1.0 O A:LEU247 3.7 17.7 1.0 CA A:ILE249 3.8 16.4 1.0 C A:ILE249 3.9 16.2 1.0 C A:GLU245 3.9 20.7 1.0 O A:HOH1004 4.0 14.8 1.0 CD A:GLU245 4.0 21.9 1.0 C A:PRO246 4.0 19.4 1.0 CA A:GLY250 4.0 16.1 1.0 C A:GLY248 4.2 16.8 1.0 CA A:GLY248 4.5 17.1 1.0 N A:PRO246 4.5 20.3 1.0 O A:PRO246 4.6 19.8 1.0 OE2 A:GLU245 4.6 22.3 1.0 CG1 A:ILE249 4.6 16.5 1.0 CG2 A:ILE249 4.6 16.4 1.0 CA A:PRO246 4.6 20.0 1.0 CB A:GLU245 4.7 21.5 1.0 C3N A:NAI901 4.8 20.2 1.0 CD1 A:TYR129 4.8 16.9 1.0 CA A:GLU245 4.9 21.3 1.0

Magnesium binding site 2 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-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-Lysine-Ne-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:25.2 occ:1.00 O7N B:NAI901 2.7 20.8 1.0 OE1 B:GLU245 2.9 23.5 1.0 N B:GLY250 3.0 16.1 1.0 OH B:TYR129 3.1 18.1 1.0 N B:ILE249 3.3 16.3 1.0 O B:GLU245 3.3 20.5 1.0 C7N B:NAI901 3.4 21.2 1.0 N7N B:NAI901 3.4 21.1 1.0 N B:LEU247 3.5 18.3 1.0 CE1 B:TYR129 3.5 18.0 1.0 C B:LEU247 3.5 17.3 1.0 CB B:ILE249 3.6 16.3 1.0 CA B:ILE249 3.7 16.2 1.0 CZ B:TYR129 3.7 18.1 1.0 CA B:LEU247 3.7 17.7 1.0 O B:LEU247 3.8 17.1 1.0 N B:GLY248 3.8 17.0 1.0 C B:ILE249 3.8 16.1 1.0 O B:HOH1002 3.9 21.1 1.0 CA B:GLY250 4.0 16.1 1.0 CD B:GLU245 4.1 22.9 1.0 C B:GLU245 4.1 20.8 1.0 C B:PRO246 4.1 19.0 1.0 C B:GLY248 4.2 16.5 1.0 CG1 B:ILE249 4.4 16.4 1.0 CA B:GLY248 4.5 16.7 1.0 O B:PRO246 4.7 18.9 1.0 N B:PRO246 4.7 20.1 1.0 CG2 B:ILE249 4.7 16.3 1.0 CB B:GLU245 4.7 22.3 1.0 CD1 B:TYR129 4.7 18.0 1.0 C3N B:NAI901 4.8 21.6 1.0 CA B:PRO246 4.8 19.6 1.0 OE2 B:GLU245 4.8 23.2 1.0 CG2 B:THR125 4.9 17.9 1.0 CA B:GLU245 5.0 21.9 1.0

Magnesium binding site 3 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg903 b:50.9 occ:1.00 OH C:TYR129 2.8 34.8 1.0 O7N C:NAI901 2.8 40.3 1.0 OE1 C:GLU245 2.8 44.1 1.0 O C:GLU245 2.9 39.1 1.0 N C:GLY250 3.2 34.5 1.0 N7N C:NAI901 3.3 38.8 1.0 N C:ILE249 3.4 36.9 1.0 C7N C:NAI901 3.4 40.1 1.0 CE1 C:TYR129 3.5 33.5 1.0 N C:LEU247 3.5 37.4 1.0 CZ C:TYR129 3.6 34.4 1.0 CB C:ILE249 3.6 36.2 1.0 C C:LEU247 3.7 37.4 1.0 C C:GLU245 3.8 39.8 1.0 CA C:ILE249 3.8 36.4 1.0 CA C:LEU247 3.9 37.6 1.0 N C:GLY248 3.9 37.7 1.0 C C:ILE249 4.0 35.5 1.0 O C:LEU247 4.0 37.1 1.0 CD C:GLU245 4.0 43.5 1.0 C C:PRO246 4.0 37.4 1.0 CA C:GLY250 4.1 34.7 1.0 O C:HOH1008 4.3 30.1 1.0 C C:GLY248 4.3 37.7 1.0 CG1 C:ILE249 4.4 36.8 1.0 CB C:GLU245 4.4 42.0 1.0 N C:PRO246 4.5 39.1 1.0 O C:PRO246 4.5 37.8 1.0 CA C:GLU245 4.6 40.9 1.0 CG2 C:ILE249 4.6 36.6 1.0 CA C:GLY248 4.6 38.0 1.0 CA C:PRO246 4.7 38.3 1.0 CD1 C:TYR129 4.7 33.8 1.0 CD1 C:ILE249 4.8 36.9 1.0 OE2 C:GLU245 4.8 43.6 1.0 C3N C:NAI901 4.8 39.5 1.0 CG C:GLU245 4.8 43.2 1.0 CE2 C:TYR129 4.9 34.8 1.0 N C:GLU245 5.0 41.1 1.0

Magnesium binding site 4 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-D-Lysine 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-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg903 b:54.6 occ:1.00 O7N D:NAI901 2.6 43.7 1.0 OE1 D:GLU245 2.9 49.4 1.0 OH D:TYR129 2.9 39.9 1.0 O D:GLU245 3.0 44.7 1.0 N D:GLY250 3.2 39.2 1.0 N D:LEU247 3.2 42.0 1.0 N D:ILE249 3.4 41.2 1.0 C7N D:NAI901 3.4 43.3 1.0 N7N D:NAI901 3.4 44.7 1.0 C D:LEU247 3.4 41.3 1.0 CA D:LEU247 3.6 41.1 1.0 CB D:ILE249 3.6 40.9 1.0 CE2 D:TYR129 3.6 38.6 1.0 N D:GLY248 3.7 41.0 1.0 O D:LEU247 3.7 40.5 1.0 CZ D:TYR129 3.7 38.8 1.0 C D:GLU245 3.8 45.8 1.0 CA D:ILE249 3.8 40.8 1.0 C D:PRO246 3.9 44.1 1.0 O D:HOH1017 4.0 38.5 1.0 C D:ILE249 4.0 39.8 1.0 CD D:GLU245 4.1 50.0 1.0 CA D:GLY250 4.1 39.5 1.0 C D:GLY248 4.3 41.9 1.0 N D:PRO246 4.4 46.0 1.0 O D:PRO246 4.4 45.4 1.0 CG1 D:ILE249 4.5 41.2 1.0 CA D:PRO246 4.5 45.5 1.0 CA D:GLY248 4.6 41.9 1.0 CB D:GLU245 4.6 47.9 1.0 CG2 D:ILE249 4.6 40.6 1.0 CA D:GLU245 4.7 46.4 1.0 C3N D:NAI901 4.8 41.3 1.0 OE2 D:GLU245 4.9 51.2 1.0 CD1 D:ILE249 4.9 41.7 1.0 CD2 D:TYR129 4.9 37.9 1.0 CG D:GLU245 5.0 48.6 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