Magnesium in PDB 4ffp: Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine)

The structure of Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine), PDB code: 4ffp was solved by F.Quitterer, A.List, 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 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.260, 61.260, 172.080, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.1

The binding sites of Magnesium atom in the Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine) (pdb code 4ffp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine), PDB code: 4ffp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:35.0 occ:1.00 O3B A:ADP902 1.7 37.4 1.0 O2A A:ADP902 1.8 39.4 1.0 OE1 A:GLU227 1.9 41.9 1.0 OE2 A:GLU239 2.1 31.8 1.0 O4 A:PO4903 2.1 36.8 1.0 O A:HOH1168 2.3 39.3 1.0 PB A:ADP902 2.9 36.4 1.0 PA A:ADP902 3.0 35.2 1.0 CD A:GLU227 3.1 43.1 1.0 CD A:GLU239 3.1 32.2 1.0 MG A:MG905 3.2 32.5 1.0 O3A A:ADP902 3.4 36.3 1.0 P A:PO4903 3.4 44.0 1.0 O1B A:ADP902 3.4 37.3 1.0 OE2 A:GLU227 3.6 50.1 1.0 O A:HOH1017 3.7 45.3 1.0 CG A:GLU239 3.7 29.9 1.0 O3 A:PO4903 3.7 37.5 1.0 O5' A:ADP902 4.0 33.0 1.0 O2B A:ADP902 4.0 32.4 1.0 C5' A:ADP902 4.1 32.0 1.0 O2 A:PO4903 4.1 48.9 1.0 OE1 A:GLU239 4.2 33.8 1.0 O1A A:ADP902 4.2 28.6 1.0 CG A:GLU227 4.4 36.1 1.0 O3' A:ADP902 4.4 27.4 1.0 OD2 A:ASP241 4.6 31.0 1.0 O1 A:PO4903 4.6 43.5 1.0 C3' A:ADP902 4.7 28.6 1.0 C4' A:ADP902 4.9 31.4 1.0

Magnesium binding site 2 out of 2 in the Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine and D-Ornithine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:32.5 occ:1.00 O1B A:ADP902 1.7 37.3 1.0 OE2 A:GLU239 1.7 31.8 1.0 OE1 A:GLU239 2.0 33.8 1.0 CD A:GLU239 2.1 32.2 1.0 O3 A:PO4903 2.1 37.5 1.0 OD2 A:ASP241 2.2 31.0 1.0 O A:HOH1203 2.4 31.0 1.0 PB A:ADP902 2.8 36.4 1.0 O3B A:ADP902 3.0 37.4 1.0 MG A:MG904 3.2 35.0 1.0 P A:PO4903 3.2 44.0 1.0 O4 A:PO4903 3.2 36.8 1.0 CG A:ASP241 3.3 29.3 1.0 CG A:GLU239 3.6 29.9 1.0 OD1 A:ASP241 3.7 30.4 1.0 NZ A:LYS104 3.7 30.7 1.0 O3A A:ADP902 3.8 36.3 1.0 O2B A:ADP902 3.8 32.4 1.0 O2A A:ADP902 4.0 39.4 1.0 O A:HOH1169 4.1 20.9 1.0 OE1 A:GLU227 4.1 41.9 1.0 O1 A:PO4903 4.2 43.5 1.0 CA A:SER136 4.2 42.0 1.0 CB A:SER136 4.3 41.6 1.0 O2 A:PO4903 4.3 48.9 1.0 CE A:LYS104 4.3 31.1 1.0 O A:GLU135 4.3 45.0 1.0 NH2 A:ARG243 4.3 35.3 1.0 O A:HOH1010 4.4 31.3 1.0 PA A:ADP902 4.4 35.2 1.0 CB A:GLU239 4.6 27.8 1.0 CB A:ASP241 4.8 24.7 1.0 N A:SER137 5.0 40.7 1.0

F.Quitterer, A.List, P.Beck, A.Bacher, M.Groll. Biosynthesis of the 22ND Genetically Encoded Amino Acid Pyrrolysine: Structure and Reaction Mechanism of Pylc at 1.5A Resolution. J.Mol.Biol. V. 424 270 2012.
ISSN: ISSN 0022-2836
PubMed: 22985965
DOI: 10.1016/J.JMB.2012.09.007