Magnesium in PDB 4j4h: Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh

The structure of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh, PDB code: 4j4h 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 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.250, 260.980, 48.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.8

The structure of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh (pdb code 4j4h). 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 in Complex with Pyrroline-Carboxy-Lysine and Nadh, PDB code: 4j4h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine 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 Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:25.0 occ:1.00 OE2 A:GLU245 2.6 22.8 1.0 O7N A:NAI901 2.6 18.9 1.0 OH A:TYR129 2.8 17.8 1.0 O A:GLU245 3.0 19.4 1.0 N A:GLY250 3.1 14.4 1.0 N A:ILE249 3.3 15.4 1.0 C7N A:NAI901 3.4 20.1 1.0 CE1 A:TYR129 3.5 17.6 1.0 N A:LEU247 3.5 18.9 1.0 C A:LEU247 3.5 17.9 1.0 CZ A:TYR129 3.6 18.1 1.0 N7N A:NAI901 3.6 18.7 1.0 CB A:ILE249 3.6 15.3 1.0 CA A:ILE249 3.7 14.8 1.0 CA A:LEU247 3.8 17.4 1.0 N A:GLY248 3.8 17.3 1.0 O A:LEU247 3.8 17.9 1.0 CD A:GLU245 3.8 21.6 1.0 C A:GLU245 3.8 20.0 1.0 C A:ILE249 3.9 14.7 1.0 C A:PRO246 4.0 19.7 1.0 O A:HOH1001 4.0 16.2 1.0 CA A:GLY250 4.1 14.3 1.0 C A:GLY248 4.2 16.0 1.0 O A:PRO246 4.5 20.2 1.0 OE1 A:GLU245 4.5 21.2 1.0 CG1 A:ILE249 4.5 15.5 1.0 N A:PRO246 4.5 19.8 1.0 CB A:GLU245 4.5 20.9 1.0 CA A:GLY248 4.5 16.6 1.0 CA A:PRO246 4.6 20.0 1.0 CG2 A:ILE249 4.7 15.5 1.0 CA A:GLU245 4.7 20.5 1.0 CD1 A:TYR129 4.8 17.0 1.0 CG A:GLU245 4.8 21.8 1.0 C3N A:NAI901 4.8 21.0 1.0 CE2 A:TYR129 4.9 18.1 1.0

Magnesium binding site 2 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine 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 Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:23.8 occ:1.00 O7N B:NAI901 2.5 19.4 1.0 OE1 B:GLU245 2.6 22.1 1.0 OH B:TYR129 3.0 16.7 1.0 O B:GLU245 3.0 17.1 1.0 N B:GLY250 3.2 14.4 1.0 N B:ILE249 3.3 15.3 1.0 N B:LEU247 3.4 16.8 1.0 C7N B:NAI901 3.4 20.5 1.0 C B:LEU247 3.4 15.7 1.0 N7N B:NAI901 3.5 20.1 1.0 CE1 B:TYR129 3.6 14.9 1.0 CB B:ILE249 3.6 15.9 1.0 CA B:LEU247 3.6 15.7 1.0 O B:LEU247 3.7 15.8 1.0 CZ B:TYR129 3.8 15.4 1.0 CA B:ILE249 3.8 15.1 1.0 N B:GLY248 3.8 15.8 1.0 CD B:GLU245 3.8 20.8 1.0 C B:GLU245 3.8 17.6 1.0 C B:PRO246 3.9 17.2 1.0 O B:HOH1001 3.9 16.4 1.0 C B:ILE249 4.0 14.7 1.0 CA B:GLY250 4.2 14.7 1.0 C B:GLY248 4.2 15.6 1.0 O B:PRO246 4.4 17.5 1.0 CG1 B:ILE249 4.4 16.9 1.0 N B:PRO246 4.4 17.7 1.0 OE2 B:GLU245 4.5 22.8 1.0 CB B:GLU245 4.5 19.0 1.0 CA B:GLY248 4.5 16.1 1.0 CA B:PRO246 4.6 17.5 1.0 CG2 B:ILE249 4.7 16.1 1.0 CA B:GLU245 4.7 18.3 1.0 CG B:GLU245 4.8 20.3 1.0 C3N B:NAI901 4.8 21.5 1.0 CD1 B:TYR129 4.9 15.8 1.0

Magnesium binding site 3 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg904 b:42.2 occ:1.00 O7N C:NAI901 2.4 34.8 1.0 OE2 C:GLU245 2.6 37.0 1.0 O C:GLU245 2.8 31.2 1.0 OH C:TYR129 3.0 31.9 1.0 C7N C:NAI901 3.2 33.5 1.0 N7N C:NAI901 3.3 32.7 1.0 N C:GLY250 3.3 29.9 1.0 N C:LEU247 3.3 30.3 1.0 N C:ILE249 3.5 32.5 1.0 C C:LEU247 3.5 29.8 1.0 CE2 C:TYR129 3.6 29.1 1.0 CA C:LEU247 3.6 30.1 1.0 C C:GLU245 3.6 30.9 1.0 O C:LEU247 3.7 29.4 1.0 CB C:ILE249 3.8 30.9 1.0 C C:PRO246 3.8 32.1 1.0 CZ C:TYR129 3.8 29.2 1.0 N C:GLY248 3.8 29.8 1.0 CD C:GLU245 3.8 32.6 1.0 CA C:ILE249 3.9 31.6 1.0 O C:HOH1002 4.0 28.8 1.0 C C:ILE249 4.1 31.0 1.0 CA C:GLY250 4.2 27.6 1.0 O C:PRO246 4.3 30.4 1.0 N C:PRO246 4.3 32.0 1.0 CB C:GLU245 4.4 31.1 1.0 C C:GLY248 4.4 33.0 1.0 CA C:PRO246 4.4 32.3 1.0 CG1 C:ILE249 4.5 30.7 1.0 OE1 C:GLU245 4.6 35.1 1.0 CA C:GLU245 4.6 31.3 1.0 CA C:GLY248 4.6 30.8 1.0 C3N C:NAI901 4.6 33.2 1.0 CG C:GLU245 4.7 30.1 1.0 CG2 C:ILE249 4.8 31.5 1.0 CD2 C:TYR129 4.9 28.4 1.0 CG2 C:THR125 5.0 28.6 1.0

Magnesium binding site 4 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg904 b:48.3 occ:1.00 O7N D:NAI901 2.6 36.8 1.0 OE2 D:GLU245 2.7 42.0 1.0 O D:GLU245 2.8 34.7 1.0 OH D:TYR129 2.8 29.2 1.0 N D:GLY250 3.2 31.8 1.0 N D:ILE249 3.4 32.8 1.0 C7N D:NAI901 3.4 33.8 1.0 N D:LEU247 3.4 33.5 1.0 N7N D:NAI901 3.5 31.7 1.0 C D:LEU247 3.5 33.8 1.0 CE1 D:TYR129 3.6 28.2 1.0 CB D:ILE249 3.6 32.8 1.0 C D:GLU245 3.6 34.6 1.0 CZ D:TYR129 3.6 29.2 1.0 CA D:LEU247 3.7 32.9 1.0 O D:LEU247 3.7 34.9 1.0 CA D:ILE249 3.8 33.1 1.0 C D:PRO246 3.8 31.7 1.0 N D:GLY248 3.9 34.1 1.0 CD D:GLU245 3.9 38.8 1.0 C D:ILE249 4.0 33.4 1.0 O D:HOH1001 4.2 25.4 1.0 CA D:GLY250 4.2 30.1 1.0 CB D:GLU245 4.3 38.1 1.0 O D:PRO246 4.3 30.0 1.0 C D:GLY248 4.3 34.8 1.0 N D:PRO246 4.3 33.7 1.0 CG1 D:ILE249 4.3 33.2 1.0 CA D:PRO246 4.5 32.5 1.0 CA D:GLU245 4.5 36.5 1.0 CA D:GLY248 4.6 35.5 1.0 CG2 D:ILE249 4.7 32.4 1.0 CG D:GLU245 4.7 38.8 1.0 OE1 D:GLU245 4.7 39.3 1.0 C3N D:NAI901 4.8 32.8 1.0 CD1 D:TYR129 4.9 29.5 1.0 CD1 D:ILE249 4.9 32.6 1.0 CE2 D:TYR129 5.0 29.5 1.0 CG2 D:THR125 5.0 32.9 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