Magnesium in PDB 5n0n: Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam

The structure of Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam, PDB code: 5n0n was solved by H.Song, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.67 / 1.76
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.304, 93.664, 165.331, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20

The binding sites of Magnesium atom in the Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam (pdb code 5n0n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam, PDB code: 5n0n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:72.1 occ:1.00 O A:HOH650 2.7 41.9 1.0 O A:HOH774 2.8 43.6 1.0 O18 A:EDT502 3.2 0.1 0.3 O20 A:EDT502 3.7 0.2 0.3 CG2 A:ILE164 3.7 43.6 1.0 C1 A:EDT502 4.3 0.2 0.3 CG1 A:ILE164 4.4 43.8 1.0 CB A:ILE164 4.6 42.9 1.0 O A:VAL162 4.7 40.5 1.0 OE1 A:GLU201 4.7 48.1 1.0 CD1 A:ILE164 4.7 45.8 1.0 O17 A:EDT502 4.8 0.6 0.3 CG2 A:VAL162 4.8 44.6 1.0 C5 A:EDT502 4.8 0.3 0.3 N A:ILE164 4.8 40.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Opha-DELTAC6 Mutant Y63F in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:35.8 occ:1.00 O A:GLY16 2.7 27.6 1.0 O A:HOH635 2.8 26.9 1.0 O A:HOH728 3.0 27.1 1.0 OG1 A:THR26 3.2 25.5 1.0 N A:THR26 3.2 25.9 1.0 C A:GLY16 3.4 26.6 1.0 CB A:ALA29 3.4 27.0 1.0 CG2 A:THR26 3.6 26.0 1.0 CB A:THR26 3.7 25.9 1.0 CA A:MET25 4.0 27.0 1.0 CA A:GLY16 4.0 25.8 1.0 CA A:THR26 4.0 25.9 1.0 C A:MET25 4.0 26.6 1.0 N A:GLY16 4.1 25.2 1.0 CA A:GLY127 4.1 25.3 1.0 N A:THR17 4.2 26.9 1.0 O A:PRO126 4.2 26.5 1.0 CG A:MET25 4.3 28.9 1.0 O A:GLN24 4.4 27.0 1.0 O A:HOH640 4.4 30.7 1.0 CA A:THR17 4.4 27.2 1.0 C A:THR17 4.6 27.2 1.0 N A:GLY18 4.7 26.3 1.0 CB A:MET25 4.7 27.8 1.0 CA A:ALA29 4.8 27.0 1.0 O A:THR26 4.9 26.0 1.0 C A:THR26 4.9 26.3 1.0 N A:GLY127 5.0 25.6 1.0 C A:PRO126 5.0 26.0 1.0

H.Song, N.S.Van Der Velden, S.L.Shiran, P.Bleiziffer, C.Zach, R.Sieber, A.S.Imani, F.Krausbeck, M.Aebi, M.F.Freeman, S.Riniker, M.Kunzler, J.H.Naismith. A Molecular Mechanism For the Enzymatic Methylation of Nitrogen Atoms Within Peptide Bonds. Sci Adv V. 4 T2720 2018.
ISSN: ESSN 2375-2548
PubMed: 30151425
DOI: 10.1126/SCIADV.AAT2720