Magnesium in PDB 4ffn: Pylc in Complex with D-Ornithine and Amppnp

The structure of Pylc in Complex with D-Ornithine and Amppnp, PDB code: 4ffn 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)	15.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.150, 60.150, 172.530, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.9

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

Magnesium binding site 1 out of 2 in the Pylc in Complex with D-Ornithine and Amppnp


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 D-Ornithine and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:39.5 occ:1.00 OE2 A:GLU239 1.9 35.6 1.0 O1A A:ANP902 1.9 37.6 1.0 OE1 A:GLU227 2.0 41.1 1.0 N3B A:ANP902 2.0 40.9 1.0 O3A A:ANP902 2.0 39.2 1.0 O3G A:ANP902 2.1 40.8 1.0 PB A:ANP902 2.4 39.5 1.0 PA A:ANP902 2.4 37.2 1.0 PG A:ANP902 2.4 44.7 1.0 MG A:MG904 2.7 38.5 1.0 CD A:GLU239 2.7 35.5 1.0 O A:HOH1148 2.8 36.1 1.0 CD A:GLU227 3.2 39.8 1.0 O2B A:ANP902 3.5 40.6 1.0 CG A:GLU239 3.5 34.6 1.0 O2G A:ANP902 3.5 41.5 1.0 OE1 A:GLU239 3.5 36.4 1.0 O5' A:ANP902 3.6 36.5 1.0 O1B A:ANP902 3.6 41.4 1.0 O2A A:ANP902 3.6 36.6 1.0 O1G A:ANP902 3.7 45.9 1.0 C5' A:ANP902 3.8 35.6 1.0 OE2 A:GLU227 3.9 43.0 1.0 OD2 A:ASP241 4.2 36.8 1.0 CG A:GLU227 4.4 38.1 1.0 O3' A:ANP902 4.5 34.4 1.0 NZ A:LYS104 4.6 38.0 1.0 C3' A:ANP902 4.7 34.0 1.0 CB A:GLU239 4.8 32.3 1.0 C4' A:ANP902 4.9 35.1 1.0 CE A:LYS104 4.9 38.1 1.0

Magnesium binding site 2 out of 2 in the Pylc in Complex with D-Ornithine and Amppnp


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 D-Ornithine and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:38.5 occ:1.00 OE2 A:GLU239 1.9 35.6 1.0 OE1 A:GLU239 1.9 36.4 1.0 OD2 A:ASP241 2.0 36.8 1.0 O2B A:ANP902 2.0 40.6 1.0 CD A:GLU239 2.1 35.5 1.0 O2G A:ANP902 2.2 41.5 1.0 PG A:ANP902 2.4 44.7 1.0 PB A:ANP902 2.5 39.5 1.0 MG A:MG903 2.7 39.5 1.0 N3B A:ANP902 2.8 40.9 1.0 O3G A:ANP902 3.0 40.8 1.0 O3A A:ANP902 3.0 39.2 1.0 CG A:ASP241 3.2 34.9 1.0 NZ A:LYS104 3.4 38.0 1.0 CG A:GLU239 3.6 34.6 1.0 OD1 A:ASP241 3.7 35.6 1.0 OE1 A:GLU227 3.8 41.1 1.0 O1B A:ANP902 3.8 41.4 1.0 O1G A:ANP902 3.9 45.9 1.0 O A:HOH1149 4.1 29.3 1.0 O A:GLU135 4.1 53.8 1.0 CB A:SER136 4.2 49.9 1.0 CA A:SER136 4.2 51.5 1.0 O1A A:ANP902 4.3 37.6 1.0 PA A:ANP902 4.3 37.2 1.0 CE A:LYS104 4.5 38.1 1.0 CB A:ASP241 4.6 33.2 1.0 CB A:GLU239 4.6 32.3 1.0 O A:HOH1010 4.6 31.4 1.0 NH2 A:ARG243 4.7 36.0 1.0 OXT A:ORD901 4.8 43.9 1.0 CD A:GLU227 4.9 39.8 1.0 O2A A:ANP902 5.0 36.6 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