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

The structure of Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine-Ne-D-Ornithine), PDB code: 4ffm 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 / 1.91
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.920, 61.920, 172.700, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.5

The binding sites of Magnesium atom in the Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine-Ne-D-Ornithine) (pdb code 4ffm). 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-Ne-D-Ornithine), PDB code: 4ffm:
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-Ne-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-Ne-D-Ornithine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:38.3 occ:1.00 O1A A:ADP902 1.8 36.3 1.0 O1B A:ADP902 1.9 36.2 1.0 OE2 A:GLU239 1.9 36.5 1.0 OE1 A:GLU227 2.0 39.9 1.0 PB A:ADP902 2.4 32.8 1.0 O A:HOH1204 2.5 32.1 1.0 PA A:ADP902 2.5 31.2 1.0 O3A A:ADP902 2.7 34.2 1.0 O A:HOH1160 2.8 43.8 1.0 CD A:GLU239 2.9 35.3 1.0 MG A:MG904 2.9 37.1 1.0 O3B A:ADP902 3.1 34.2 1.0 CD A:GLU227 3.2 38.0 1.0 O2A A:ADP902 3.5 29.5 1.0 CG A:GLU239 3.6 33.3 1.0 OE1 A:GLU239 3.8 34.3 1.0 O2B A:ADP902 3.8 33.1 1.0 O5' A:ADP902 3.8 29.7 1.0 O A:HOH1226 3.8 40.9 1.0 OE2 A:GLU227 3.9 43.7 1.0 C5' A:ADP902 4.1 25.3 1.0 OD2 A:ASP241 4.3 33.4 1.0 CG A:GLU227 4.5 34.5 1.0 O A:HOH1016 4.8 54.3 1.0 O3' A:ADP902 4.9 26.9 1.0 CB A:GLU239 4.9 31.1 1.0

Magnesium binding site 2 out of 2 in the Pylc in Complex with L-Lysine-Ne-D-Ornithine (Cocrystallized with L- Lysine-Ne-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-Ne-D-Ornithine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:37.1 occ:1.00 OE2 A:GLU239 1.9 36.5 1.0 O3B A:ADP902 1.9 34.2 1.0 OE1 A:GLU239 1.9 34.3 1.0 OD2 A:ASP241 2.0 33.4 1.0 CD A:GLU239 2.1 35.3 1.0 O A:HOH1226 2.1 40.9 1.0 O A:HOH1192 2.5 33.6 1.0 PB A:ADP902 2.5 32.8 1.0 O1B A:ADP902 2.8 36.2 1.0 MG A:MG903 2.9 38.3 1.0 CG A:ASP241 3.2 28.6 1.0 O A:HOH1204 3.3 32.1 1.0 OD1 A:ASP241 3.6 29.0 1.0 CG A:GLU239 3.6 33.3 1.0 O2B A:ADP902 3.7 33.1 1.0 O3A A:ADP902 3.8 34.2 1.0 NZ A:LYS104 3.9 35.0 1.0 OE1 A:GLU227 4.0 39.9 1.0 O A:HOH1161 4.2 25.7 1.0 CE A:LYS104 4.3 37.1 1.0 NH2 A:ARG243 4.4 35.0 1.0 O1A A:ADP902 4.5 36.3 1.0 PA A:ADP902 4.5 31.2 1.0 O A:HOH1010 4.6 40.5 1.0 CB A:GLU239 4.6 31.1 1.0 CB A:ASP241 4.6 26.6 1.0 O2A A:ADP902 5.0 29.5 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