Magnesium in PDB 8xdq: O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah

The structure of O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah, PDB code: 8xdq was solved by Y.Y.H.Saw, Y.Nakashima, H.Morita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.08 / 1.77
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.766, 81.374, 119.205, 90, 90, 90
R / Rfree (%)	16.2 / 19

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah (pdb code 8xdq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah, PDB code: 8xdq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:18.4 occ:1.00 OD2 A:ASP181 2.0 17.5 1.0 O A:HOH705 2.1 14.9 1.0 O A:HOH818 2.1 19.4 1.0 OD1 A:ASN182 2.2 17.4 1.0 OD1 A:ASP155 2.2 17.1 1.0 O A:HOH839 2.2 19.1 1.0 CG A:ASP155 3.0 18.6 1.0 CG A:ASP181 3.1 16.2 1.0 CG A:ASN182 3.1 17.9 1.0 OD2 A:ASP155 3.2 17.1 1.0 ND2 A:ASN182 3.5 16.9 1.0 CB A:ASP181 3.6 15.7 1.0 NZ A:LYS158 4.0 27.2 1.0 O A:ALA53 4.1 17.0 1.0 OD1 A:ASP181 4.1 19.9 1.0 O A:HOH742 4.3 22.6 1.0 O A:HOH876 4.4 28.2 1.0 O A:HOH780 4.4 18.8 1.0 CB A:ASP155 4.5 19.0 1.0 CB A:ASN182 4.5 16.3 1.0 O A:HOH735 4.6 22.7 1.0 N A:ASN182 4.7 15.2 1.0 C A:ASP181 4.8 14.7 1.0 CA A:ASP181 4.8 13.5 1.0 CG2 A:VAL55 4.9 16.3 1.0 CA A:VAL55 4.9 15.2 1.0 O A:ASP155 5.0 20.8 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of O-Methyltransferase From Lycoris Aurea Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:19.7 occ:1.00 OD2 B:ASP181 2.0 20.7 1.0 O B:HOH405 2.1 18.1 1.0 O B:HOH506 2.1 24.6 1.0 OD1 B:ASN182 2.1 20.5 1.0 OD1 B:ASP155 2.2 19.0 1.0 O B:HOH495 2.2 24.8 1.0 CG B:ASP155 3.0 17.8 1.0 CG B:ASP181 3.0 21.9 1.0 CG B:ASN182 3.1 18.7 1.0 OD2 B:ASP155 3.2 20.7 1.0 ND2 B:ASN182 3.5 18.1 1.0 CB B:ASP181 3.6 16.1 1.0 NZ B:LYS158 3.9 34.9 1.0 O B:ALA53 4.0 19.2 1.0 OD1 B:ASP181 4.1 23.1 1.0 O B:HOH563 4.3 33.5 1.0 O B:HOH423 4.4 25.6 1.0 CB B:ASP155 4.4 16.9 1.0 CB B:ASN182 4.5 17.2 1.0 O B:HOH489 4.5 25.8 1.0 O B:HOH436 4.7 26.7 1.0 N B:ASN182 4.8 15.2 1.0 C B:ASP181 4.8 14.9 1.0 CA B:ASP181 4.9 15.2 1.0 CA B:VAL55 5.0 17.9 1.0 CA B:ASP155 5.0 17.9 1.0 O B:ASP155 5.0 24.0 1.0 CE B:LYS158 5.0 33.7 1.0

S.Y.Y.Hnin, Y.Nakashima, T.Kodama, H.Morita. Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases Acs Catalysis 11865 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C03305