Magnesium in PDB 4q3c: Pyld Cocrystallized with L-Lysine-Ne-L-Lysine and Nad+

The structure of Pyld Cocrystallized with L-Lysine-Ne-L-Lysine and Nad+, PDB code: 4q3c 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 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.250, 259.770, 48.930, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.8

The structure of Pyld Cocrystallized with L-Lysine-Ne-L-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-L-Lysine and Nad+ (pdb code 4q3c). 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-L-Lysine and Nad+, PDB code: 4q3c:
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-L-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-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:39.1 occ:1.00 O7N A:NAD901 2.5 28.6 1.0 OE1 A:GLU245 2.8 29.1 1.0 OH A:TYR129 3.0 25.9 1.0 O A:GLU245 3.1 25.7 1.0 N A:GLY250 3.1 18.8 1.0 C7N A:NAD901 3.3 25.1 1.0 N A:LEU247 3.3 23.7 1.0 N7N A:NAD901 3.4 26.1 1.0 N A:ILE249 3.4 20.9 1.0 C A:LEU247 3.5 22.1 1.0 CE2 A:TYR129 3.6 21.0 1.0 CA A:LEU247 3.6 20.9 1.0 N A:GLY248 3.7 22.4 1.0 CB A:ILE249 3.7 20.2 1.0 CZ A:TYR129 3.8 21.6 1.0 O A:LEU247 3.8 19.3 1.0 C A:PRO246 3.8 22.3 1.0 CA A:ILE249 3.9 19.3 1.0 C A:GLU245 3.9 24.1 1.0 CD A:GLU245 4.0 25.5 1.0 C A:ILE249 4.0 19.2 1.0 O A:HOH1005 4.0 24.1 1.0 CA A:GLY250 4.1 19.9 1.0 C A:GLY248 4.2 21.1 1.0 O A:PRO246 4.3 24.1 1.0 CA A:PRO246 4.5 21.7 1.0 N A:PRO246 4.5 23.5 1.0 CA A:GLY248 4.5 20.6 1.0 OE2 A:GLU245 4.6 29.3 1.0 CG1 A:ILE249 4.7 19.7 1.0 CB A:GLU245 4.7 21.6 1.0 C3N A:NAD901 4.7 24.5 1.0 CG2 A:ILE249 4.7 21.0 1.0 CA A:GLU245 4.9 22.0 1.0 CD2 A:TYR129 4.9 21.0 1.0 CG A:GLU245 5.0 22.2 1.0

Magnesium binding site 2 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-L-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-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:38.9 occ:1.00 O7N B:NAD901 2.7 29.6 1.0 OH B:TYR129 2.9 23.9 1.0 OE1 B:GLU245 2.9 28.0 1.0 N B:GLY250 3.1 18.6 1.0 O B:GLU245 3.2 22.9 1.0 N7N B:NAD901 3.4 23.3 1.0 N B:ILE249 3.4 19.6 1.0 C7N B:NAD901 3.4 25.9 1.0 CE1 B:TYR129 3.4 20.6 1.0 N B:LEU247 3.5 21.6 1.0 CB B:ILE249 3.6 19.5 1.0 CZ B:TYR129 3.6 21.4 1.0 C B:LEU247 3.6 21.5 1.0 CA B:ILE249 3.8 19.4 1.0 CA B:LEU247 3.8 21.2 1.0 N B:GLY248 3.9 22.7 1.0 O B:LEU247 3.9 20.0 1.0 C B:ILE249 3.9 20.3 1.0 C B:GLU245 4.0 22.9 1.0 O B:HOH1017 4.0 25.6 1.0 C B:PRO246 4.0 20.7 1.0 CA B:GLY250 4.1 19.1 1.0 CD B:GLU245 4.1 22.9 1.0 C B:GLY248 4.3 21.2 1.0 N B:PRO246 4.5 22.6 1.0 CG1 B:ILE249 4.5 18.7 1.0 O B:PRO246 4.5 25.8 1.0 CG2 B:ILE249 4.6 19.5 1.0 CA B:GLY248 4.6 21.2 1.0 CA B:PRO246 4.7 21.2 1.0 CD1 B:TYR129 4.7 20.8 1.0 OE2 B:GLU245 4.8 25.2 1.0 CB B:GLU245 4.8 22.1 1.0 C3N B:NAD901 4.8 25.0 1.0 CA B:GLU245 4.9 21.9 1.0 CE2 B:TYR129 5.0 20.1 1.0

Magnesium binding site 3 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-L-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-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg903 b:82.5 occ:1.00 O C:GLU245 2.7 55.3 1.0 OE1 C:GLU245 2.8 64.3 1.0 OH C:TYR129 2.8 53.0 1.0 O7N C:NAD901 2.8 68.3 1.0 N C:LEU247 3.3 52.0 1.0 N7N C:NAD901 3.3 58.7 1.0 N C:GLY250 3.4 43.7 1.0 C7N C:NAD901 3.5 67.3 1.0 C C:LEU247 3.5 55.4 1.0 O C:LEU247 3.5 69.3 1.0 N C:ILE249 3.5 51.1 1.0 CE1 C:TYR129 3.6 45.6 1.0 CB C:ILE249 3.6 48.9 1.0 CZ C:TYR129 3.6 46.6 1.0 CA C:LEU247 3.6 49.5 1.0 C C:GLU245 3.7 55.3 1.0 C C:PRO246 3.8 54.4 1.0 CA C:ILE249 3.9 46.4 1.0 CD C:GLU245 4.0 71.5 1.0 N C:GLY248 4.0 52.0 1.0 C C:ILE249 4.1 43.8 1.0 O C:HOH1010 4.2 55.5 1.0 O C:PRO246 4.3 54.5 1.0 CA C:GLY250 4.3 43.0 1.0 N C:PRO246 4.4 61.7 1.0 C C:GLY248 4.4 50.4 1.0 CA C:PRO246 4.4 57.8 1.0 CG1 C:ILE249 4.5 52.1 1.0 CG2 C:ILE249 4.6 50.0 1.0 CB C:GLU245 4.6 61.2 1.0 CA C:GLU245 4.7 56.0 1.0 OE2 C:GLU245 4.7 83.0 1.0 CA C:GLY248 4.7 51.1 1.0 CD1 C:TYR129 4.9 44.8 1.0 C3N C:NAD901 4.9 64.2 1.0 CG C:GLU245 4.9 63.5 1.0 CE2 C:TYR129 5.0 44.3 1.0 CD1 C:ILE249 5.0 50.3 1.0

Magnesium binding site 4 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-L-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-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg903 b:85.0 occ:1.00 O D:GLU245 2.5 63.1 1.0 OE1 D:GLU245 2.6 82.8 1.0 OH D:TYR129 2.9 58.7 1.0 N D:LEU247 2.9 60.5 1.0 O7N D:NAD901 3.0 95.6 1.0 C D:LEU247 3.2 56.9 1.0 C D:GLU245 3.3 66.6 1.0 N D:ILE249 3.3 56.3 1.0 N D:GLY248 3.4 58.5 1.0 CA D:LEU247 3.4 54.9 1.0 N7N D:NAD901 3.6 77.4 1.0 N D:GLY250 3.6 57.4 1.0 C D:PRO246 3.6 67.3 1.0 O D:LEU247 3.7 55.2 1.0 CD D:GLU245 3.7 81.8 1.0 C7N D:NAD901 3.7 83.1 1.0 CB D:ILE249 3.8 53.5 1.0 CZ D:TYR129 3.9 58.5 1.0 CA D:ILE249 4.0 55.5 1.0 N D:PRO246 4.0 72.6 1.0 CE1 D:TYR129 4.0 55.6 1.0 CB D:GLU245 4.1 71.3 1.0 CA D:PRO246 4.2 70.8 1.0 C D:GLY248 4.2 53.5 1.0 CA D:GLU245 4.2 67.8 1.0 CA D:GLY248 4.3 54.6 1.0 C D:ILE249 4.3 55.1 1.0 O D:PRO246 4.4 74.2 1.0 CG1 D:ILE249 4.4 56.8 1.0 O D:HOH1005 4.4 52.8 1.0 OE2 D:GLU245 4.5 87.7 1.0 CG D:GLU245 4.6 73.5 1.0 CA D:GLY250 4.6 61.0 1.0 N D:GLU245 4.7 63.3 1.0 CB D:LEU247 4.9 56.6 1.0 CD1 D:ILE249 5.0 59.0 1.0 CG2 D:ILE249 5.0 53.6 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