Magnesium in PDB 4jk3: Pyld Holoenzyme (Semet)

The structure of Pyld Holoenzyme (Semet), PDB code: 4jk3 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 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.650, 155.400, 39.570, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.7

The structure of Pyld Holoenzyme (Semet) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Pyld Holoenzyme (Semet) (pdb code 4jk3). 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 Holoenzyme (Semet), PDB code: 4jk3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyld Holoenzyme (Semet)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyld Holoenzyme (Semet) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:49.2 occ:1.00 O7N A:NAD901 2.7 36.1 1.0 OE2 A:GLU245 2.7 45.7 1.0 OH A:TYR129 2.9 27.2 1.0 N A:GLY250 3.0 29.6 1.0 O A:GLU245 3.1 39.5 1.0 N A:ILE249 3.2 30.4 1.0 C7N A:NAD901 3.5 36.7 1.0 N A:LEU247 3.5 38.2 1.0 C A:LEU247 3.5 35.6 1.0 CB A:ILE249 3.5 30.6 1.0 CE1 A:TYR129 3.6 26.9 1.0 N7N A:NAD901 3.6 35.3 1.0 CA A:ILE249 3.7 30.1 1.0 CZ A:TYR129 3.7 27.1 1.0 CA A:LEU247 3.8 37.0 1.0 O A:LEU247 3.8 35.3 1.0 C A:ILE249 3.8 30.3 1.0 N A:GLY248 3.8 34.2 1.0 C A:GLU245 3.9 40.3 1.0 CD A:GLU245 3.9 43.4 1.0 CA A:GLY250 4.0 31.1 1.0 C A:PRO246 4.1 40.2 1.0 C A:GLY248 4.1 32.1 1.0 O A:HOH1011 4.3 36.3 1.0 CG1 A:ILE249 4.3 31.2 1.0 CB A:GLU245 4.4 39.9 1.0 CA A:GLY248 4.5 32.1 1.0 N A:PRO246 4.5 41.1 1.0 O A:PRO246 4.6 42.4 1.0 CG2 A:ILE249 4.6 29.9 1.0 CA A:GLU245 4.6 39.8 1.0 CA A:PRO246 4.7 40.5 1.0 OE1 A:GLU245 4.7 42.8 1.0 CG A:GLU245 4.8 43.0 1.0 CD1 A:ILE249 4.8 30.0 1.0 C3N A:NAD901 4.9 35.7 1.0 CD1 A:TYR129 4.9 27.0 1.0 CG2 A:THR125 5.0 26.4 1.0

Magnesium binding site 2 out of 2 in the Pyld Holoenzyme (Semet)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyld Holoenzyme (Semet) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:60.0 occ:1.00 O7N B:NAD901 2.7 43.9 1.0 N B:GLY250 2.8 43.6 1.0 OE2 B:GLU245 2.9 70.9 1.0 OH B:TYR129 3.1 46.9 1.0 N B:ILE249 3.2 52.3 1.0 O B:GLU245 3.3 59.2 1.0 C7N B:NAD901 3.4 42.5 1.0 N7N B:NAD901 3.4 42.8 1.0 C B:LEU247 3.5 53.8 1.0 CB B:ILE249 3.5 53.0 1.0 CA B:ILE249 3.6 51.5 1.0 C B:ILE249 3.6 48.4 1.0 N B:LEU247 3.6 57.7 1.0 O B:LEU247 3.6 55.1 1.0 CE1 B:TYR129 3.7 43.5 1.0 CA B:GLY250 3.7 43.5 1.0 CA B:LEU247 3.7 53.7 1.0 N B:GLY248 3.8 56.0 1.0 CZ B:TYR129 3.9 44.9 1.0 C B:GLY248 4.1 53.5 1.0 CD B:GLU245 4.1 69.7 1.0 C B:GLU245 4.1 63.5 1.0 C B:PRO246 4.2 61.1 1.0 CG1 B:ILE249 4.4 53.5 1.0 CA B:GLY248 4.5 56.2 1.0 CG2 B:ILE249 4.5 53.0 1.0 CB B:GLU245 4.6 65.5 1.0 O B:PRO246 4.7 61.6 1.0 C3N B:NAD901 4.8 41.4 1.0 N B:PRO246 4.8 64.9 1.0 O B:ILE249 4.8 49.3 1.0 OE1 B:GLU245 4.9 71.6 1.0 CG2 B:THR125 4.9 37.3 1.0 CA B:PRO246 4.9 63.0 1.0 CA B:GLU245 4.9 63.9 1.0 C B:GLY250 4.9 43.7 1.0 N B:THR251 4.9 45.7 1.0 O B:GLY248 4.9 54.0 1.0 CD1 B:ILE249 5.0 53.9 1.0 CD1 B:TYR129 5.0 41.7 1.0 CG B:GLU245 5.0 69.3 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