Magnesium in PDB 5n0x: Crystal Structure of Opha-DELTAC6 in Complex with Sam

The structure of Crystal Structure of Opha-DELTAC6 in Complex with Sam, PDB code: 5n0x 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)	78.04 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.740, 101.960, 121.266, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of Opha-DELTAC6 in Complex with Sam (pdb code 5n0x). 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 in Complex with Sam, PDB code: 5n0x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Opha-DELTAC6 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 in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:48.3 occ:1.00 O A:PHE135 2.6 19.0 1.0 O A:ILE140 2.7 21.6 1.0 C A:PHE135 3.1 18.7 1.0 CE1 B:HIS109 3.2 24.7 1.0 SD B:MET124 3.5 21.3 1.0 O B:GLY102 3.6 21.2 1.0 CA B:GLY102 3.7 19.5 1.0 N A:ALA136 3.7 18.1 1.0 CB A:PHE135 3.7 18.5 1.0 C A:ILE140 3.8 22.8 1.0 ND1 B:HIS109 3.8 25.3 1.0 CA A:ALA136 3.9 18.7 1.0 N A:ILE140 3.9 23.6 1.0 CE B:MET124 3.9 22.2 1.0 CA A:PHE135 3.9 18.3 1.0 C B:GLY102 4.1 19.8 1.0 O A:HOH691 4.2 36.7 1.0 O B:HOH661 4.3 30.3 1.0 NE2 B:HIS109 4.4 26.0 1.0 CE1 B:HIS100 4.5 16.8 1.0 CA A:CYS139 4.5 24.9 1.0 C A:CYS139 4.5 24.4 1.0 CA A:ILE140 4.5 23.6 1.0 N A:ASP141 4.7 21.9 1.0 C A:ALA136 4.7 19.4 1.0 N B:GLY102 4.8 18.9 1.0 O A:ALA136 4.9 20.6 1.0 N A:CYS139 4.9 23.2 1.0 CA A:ASP141 4.9 21.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Opha-DELTAC6 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 in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:54.2 occ:1.00 O B:PHE135 2.7 20.5 1.0 O B:ILE140 3.0 22.8 1.0 C B:PHE135 3.0 20.3 1.0 SD A:MET124 3.2 21.7 1.0 CE1 A:HIS109 3.3 26.8 1.0 CA A:GLY102 3.5 20.1 1.0 N B:ALA136 3.5 19.8 1.0 CB B:PHE135 3.5 19.7 1.0 O A:GLY102 3.6 21.7 1.0 CA B:ALA136 3.7 20.4 1.0 CA B:PHE135 3.8 19.9 1.0 CE A:MET124 3.9 22.5 1.0 C A:GLY102 3.9 20.1 1.0 CE1 A:HIS100 3.9 17.7 1.0 C B:ILE140 4.1 23.7 1.0 ND1 A:HIS109 4.2 27.6 1.0 NE2 A:HIS109 4.2 27.1 1.0 N B:ILE140 4.4 24.8 1.0 N A:GLY102 4.5 19.0 1.0 O B:HOH686 4.5 37.9 1.0 C B:ALA136 4.7 21.6 1.0 CB B:ALA136 4.7 20.1 1.0 ND1 A:HIS100 4.7 17.3 1.0 NE2 A:HIS100 4.8 17.2 1.0 O A:HOH626 4.8 29.9 1.0 CG A:MET124 4.8 22.0 1.0 CG B:PHE135 4.8 20.2 1.0 CA B:CYS139 4.9 26.6 1.0 O B:ALA136 4.9 22.2 1.0 CA B:ILE140 4.9 24.7 1.0 C B:CYS139 5.0 26.1 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