Magnesium in PDB 4ffo: Pylc in Complex with Phosphorylated D-Ornithine

The structure of Pylc in Complex with Phosphorylated D-Ornithine, PDB code: 4ffo 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 (°)	61.430, 61.430, 172.020, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20

The binding sites of Magnesium atom in the Pylc in Complex with Phosphorylated D-Ornithine (pdb code 4ffo). 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 Phosphorylated D-Ornithine, PDB code: 4ffo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pylc in Complex with Phosphorylated 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 Phosphorylated D-Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:24.9 occ:1.00 O1A A:ADP902 1.9 24.1 1.0 O1B A:ADP902 1.9 24.9 1.0 OE2 A:GLU239 1.9 22.2 1.0 OE1 A:GLU227 1.9 27.4 1.0 O13 A:0TK901 2.1 28.3 1.0 PB A:ADP902 2.4 23.6 1.0 PA A:ADP902 2.5 21.5 1.0 O3A A:ADP902 2.5 22.4 1.0 O A:HOH1211 2.7 30.0 1.0 CD A:GLU239 2.8 21.2 1.0 MG A:MG904 3.0 22.8 1.0 CD A:GLU227 3.1 32.2 1.0 P11 A:0TK901 3.4 36.1 1.0 O3B A:ADP902 3.5 23.7 1.0 CG A:GLU239 3.5 21.1 1.0 O5' A:ADP902 3.6 20.0 1.0 O2B A:ADP902 3.6 22.0 1.0 O2A A:ADP902 3.7 19.3 1.0 O12 A:0TK901 3.7 26.1 1.0 OE1 A:GLU239 3.7 22.6 1.0 OE2 A:GLU227 3.7 39.1 1.0 C5' A:ADP902 3.8 20.0 1.0 O14 A:0TK901 4.0 38.1 1.0 O A:HOH1019 4.2 38.7 1.0 O A:HOH1204 4.3 37.5 1.0 CG A:GLU227 4.4 30.0 1.0 OD2 A:ASP241 4.4 23.8 1.0 O3' A:ADP902 4.4 20.0 1.0 C3' A:ADP902 4.6 19.9 1.0 CB A:GLU239 4.7 21.0 1.0 O10 A:0TK901 4.8 34.9 1.0 C4' A:ADP902 4.8 19.4 1.0 CB A:GLU227 5.0 24.8 1.0

Magnesium binding site 2 out of 2 in the Pylc in Complex with Phosphorylated 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 Phosphorylated D-Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:22.8 occ:1.00 OE2 A:GLU239 1.9 22.2 1.0 O3B A:ADP902 1.9 23.7 1.0 OE1 A:GLU239 1.9 22.6 1.0 OD2 A:ASP241 2.0 23.8 1.0 CD A:GLU239 2.1 21.2 1.0 O12 A:0TK901 2.2 26.1 1.0 O A:HOH1236 2.4 24.9 1.0 PB A:ADP902 2.5 23.6 1.0 O1B A:ADP902 2.8 24.9 1.0 MG A:MG903 3.0 24.9 1.0 O13 A:0TK901 3.1 28.3 1.0 CG A:ASP241 3.1 21.9 1.0 P11 A:0TK901 3.2 36.1 1.0 O3A A:ADP902 3.5 22.4 1.0 OD1 A:ASP241 3.6 22.3 1.0 CG A:GLU239 3.6 21.1 1.0 O2B A:ADP902 3.8 22.0 1.0 NZ A:LYS104 3.9 19.9 1.0 O A:HOH1204 3.9 37.5 1.0 OE1 A:GLU227 4.0 27.4 1.0 O A:HOH1212 4.1 15.6 1.0 NH2 A:ARG243 4.2 32.8 1.0 O14 A:0TK901 4.3 38.1 1.0 O10 A:0TK901 4.3 34.9 1.0 CE A:LYS104 4.3 20.9 1.0 CB A:SER136 4.4 35.9 1.0 O A:GLU135 4.4 37.7 1.0 PA A:ADP902 4.4 21.5 1.0 CA A:SER136 4.4 35.6 1.0 O A:HOH1010 4.5 20.0 1.0 CB A:ASP241 4.5 19.9 1.0 CB A:GLU239 4.5 21.0 1.0 O1A A:ADP902 4.5 24.1 1.0 CD A:GLU227 5.0 32.2 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