Magnesium in PDB 4ffl: Pylc in Complex with L-Lysine

The structure of Pylc in Complex with L-Lysine, PDB code: 4ffl 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 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.190, 61.190, 171.830, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.3

The binding sites of Magnesium atom in the Pylc in Complex with L-Lysine (pdb code 4ffl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pylc in Complex with L-Lysine, PDB code: 4ffl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pylc in Complex with L-Lysine


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:13.2 occ:1.00 O3B A:ADP902 2.1 13.5 1.0 OE2 A:GLU239 2.1 12.3 1.0 O2A A:ADP902 2.1 13.3 1.0 O4 A:PO4903 2.1 14.3 1.0 OE1 A:GLU227 2.2 15.7 1.0 O A:HOH1283 2.3 15.4 1.0 PB A:ADP902 2.6 14.0 1.0 O3A A:ADP902 3.1 13.1 1.0 PA A:ADP902 3.1 13.0 1.0 CD A:GLU239 3.1 11.8 1.0 MG A:MG905 3.2 13.4 1.0 CD A:GLU227 3.3 16.1 1.0 P A:PO4903 3.4 14.3 1.0 O3 A:PO4903 3.6 13.8 1.0 OE2 A:GLU227 3.7 18.0 1.0 CG A:GLU239 3.7 11.3 1.0 O1B A:ADP902 3.7 13.2 1.0 O A:HOH1019 3.8 20.1 1.0 O2B A:ADP902 3.8 13.1 1.0 MG A:MG906 3.9 17.3 1.0 C5' A:ADP902 4.0 12.2 1.0 O5' A:ADP902 4.1 12.2 1.0 O2 A:PO4903 4.1 15.6 1.0 OE1 A:GLU239 4.1 12.5 1.0 O1A A:ADP902 4.3 13.6 1.0 O A:HOH1270 4.3 17.0 1.0 O3' A:ADP902 4.4 14.9 1.0 O1 A:PO4903 4.5 15.1 1.0 OD2 A:ASP241 4.5 13.7 1.0 CG A:GLU227 4.6 15.6 1.0 O2 A:CO3907 4.7 23.2 1.0 C3' A:ADP902 4.8 12.7 1.0 O A:HOH1087 4.8 29.3 1.0 CB A:GLU227 4.9 14.2 1.0 C4' A:ADP902 4.9 12.7 1.0

Magnesium binding site 2 out of 3 in the Pylc in Complex with L-Lysine


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:13.4 occ:1.00 OE2 A:GLU239 2.1 12.3 1.0 O1B A:ADP902 2.1 13.2 1.0 OE1 A:GLU239 2.1 12.5 1.0 O3 A:PO4903 2.2 13.8 1.0 CD A:GLU239 2.2 11.8 1.0 OD2 A:ASP241 2.2 13.7 1.0 O A:HOH1281 2.3 13.4 1.0 PB A:ADP902 2.6 14.0 1.0 O3B A:ADP902 3.2 13.5 1.0 MG A:MG904 3.2 13.2 1.0 CG A:ASP241 3.3 12.7 1.0 P A:PO4903 3.3 14.3 1.0 O4 A:PO4903 3.4 14.3 1.0 OD1 A:ASP241 3.6 13.1 1.0 O3A A:ADP902 3.7 13.1 1.0 CG A:GLU239 3.7 11.3 1.0 NZ A:LYS104 3.8 14.2 1.0 O2B A:ADP902 3.9 13.1 1.0 O A:HOH1285 4.1 8.2 1.0 NH2 A:ARG243 4.1 14.1 1.0 O A:HOH1270 4.1 17.0 1.0 O A:GLU135 4.2 18.2 1.0 CA A:SER136 4.3 15.5 1.0 O1 A:PO4903 4.3 15.1 1.0 O2 A:PO4903 4.3 15.6 1.0 CB A:SER136 4.4 16.0 1.0 O A:HOH1010 4.4 14.0 1.0 CE A:LYS104 4.5 14.6 1.0 OE1 A:GLU227 4.5 15.7 1.0 O2A A:ADP902 4.5 13.3 1.0 CB A:ASP241 4.7 12.8 1.0 MG A:MG906 4.7 17.3 1.0 PA A:ADP902 4.7 13.0 1.0 CB A:GLU239 4.7 11.2 1.0 CZ A:ARG243 5.0 13.7 1.0 N A:SER137 5.0 15.9 1.0

Magnesium binding site 3 out of 3 in the Pylc in Complex with L-Lysine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pylc in Complex with L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg906 b:17.3 occ:1.00 O1 A:PO4903 1.9 15.1 1.0 O A:HOH1270 2.1 17.0 1.0 O A:HOH1243 2.1 24.2 1.0 O4 A:PO4903 2.1 14.3 1.0 OE2 A:GLU227 2.2 18.0 1.0 O2 A:CO3907 2.2 23.2 1.0 P A:PO4903 2.4 14.3 1.0 CD A:GLU227 3.1 16.1 1.0 C A:CO3907 3.2 31.5 1.0 OE1 A:GLU227 3.5 15.7 1.0 O2 A:PO4903 3.5 15.6 1.0 O3 A:PO4903 3.6 13.8 1.0 O A:HOH1069 3.6 23.3 1.0 O1 A:CO3907 3.7 35.6 1.0 OD1 A:ASP225 3.8 23.4 1.0 MG A:MG904 3.9 13.2 1.0 OE2 A:GLU239 3.9 12.3 1.0 O3 A:CO3907 4.0 38.9 1.0 NH1 A:ARG243 4.1 14.3 1.0 O A:HOH1087 4.2 29.3 1.0 OD2 A:ASP241 4.3 13.7 1.0 NZ A:LYS901 4.3 17.0 1.0 O A:HOH1283 4.3 15.4 1.0 CG A:GLU227 4.4 15.6 1.0 OD2 A:ASP225 4.4 19.1 1.0 CG A:ASP225 4.5 19.5 1.0 MG A:MG905 4.7 13.4 1.0 O3B A:ADP902 4.7 13.5 1.0 NH2 A:ARG243 4.9 14.1 1.0 CZ A:ARG243 5.0 13.7 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