Magnesium in PDB 8xdr: O-Methyltransferase From Lycoris Aurea Complexed with Mg, Sah, and 3, 4-Dihydroxybenzaldehyde

The structure of O-Methyltransferase From Lycoris Aurea Complexed with Mg, Sah, and 3, 4-Dihydroxybenzaldehyde, PDB code: 8xdr 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)	47.38 / 1.83
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.373, 81.091, 116.77, 90, 90, 90
R / Rfree (%)	16.7 / 20.5

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Aurea Complexed with Mg, Sah, and 3, 4-Dihydroxybenzaldehyde (pdb code 8xdr). 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, Sah, and 3, 4-Dihydroxybenzaldehyde, PDB code: 8xdr:
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, Sah, and 3, 4-Dihydroxybenzaldehyde


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, Sah, and 3, 4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:22.5 occ:1.00 OD2 A:ASP181 2.0 20.1 1.0 O A:HOH414 2.1 20.6 1.0 OD1 A:ASN182 2.1 20.3 1.0 OD1 A:ASP155 2.1 18.9 1.0 O A:HOH459 2.1 24.8 1.0 O A:HOH517 2.1 27.3 1.0 CG A:ASP155 3.0 20.7 1.0 CG A:ASP181 3.0 20.6 1.0 CG A:ASN182 3.1 20.9 1.0 OD2 A:ASP155 3.2 20.2 1.0 ND2 A:ASN182 3.5 23.1 1.0 CB A:ASP181 3.5 15.7 1.0 NZ A:LYS158 3.8 26.7 1.0 O A:ALA53 4.1 20.5 1.0 OD1 A:ASP181 4.1 25.7 1.0 O A:HOH573 4.3 33.2 1.0 CB A:ASP155 4.4 21.2 1.0 O A:HOH444 4.4 24.4 1.0 O A:HOH430 4.5 23.5 1.0 CB A:ASN182 4.5 19.1 1.0 N A:ASN182 4.7 15.2 1.0 C A:ASP181 4.7 16.2 1.0 CA A:ASP181 4.8 15.2 1.0 O A:HOH427 4.8 25.1 1.0 CA A:ASP155 4.9 19.7 1.0 O A:ASP155 4.9 23.9 1.0 CG2 A:VAL55 4.9 17.9 1.0 CA A:VAL55 4.9 16.4 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Aurea Complexed with Mg, Sah, and 3, 4-Dihydroxybenzaldehyde


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, Sah, and 3, 4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:24.6 occ:1.00 OD2 B:ASP181 2.0 24.4 1.0 OD1 B:ASP155 2.0 20.6 1.0 O4 B:H6N704 2.1 28.1 1.0 O B:HOH822 2.1 23.2 1.0 OD1 B:ASN182 2.2 23.0 1.0 O3 B:H6N704 2.3 29.2 1.0 CG B:ASP155 3.0 20.2 1.0 C4 B:H6N704 3.0 28.2 1.0 CG B:ASP181 3.1 25.8 1.0 CG B:ASN182 3.1 24.1 1.0 C3 B:H6N704 3.1 30.7 1.0 OD2 B:ASP155 3.2 19.5 1.0 ND2 B:ASN182 3.4 22.5 1.0 CB B:ASP181 3.7 19.0 1.0 NZ B:LYS158 3.9 27.0 1.0 O B:HOH898 3.9 26.7 1.0 O B:ALA53 4.0 22.5 1.0 OD1 B:ASP181 4.1 28.9 1.0 NZ B:LYS13 4.1 33.7 1.0 C5 B:H6N704 4.4 28.8 1.0 CB B:ASP155 4.4 18.6 1.0 C2 B:H6N704 4.5 32.4 1.0 CB B:ASN182 4.5 21.0 1.0 CE B:LYS158 4.7 27.9 1.0 O B:ASP155 4.8 22.7 1.0 C B:ASP181 4.8 19.7 1.0 CA B:ASP155 4.8 18.6 1.0 N B:ASN182 4.9 19.2 1.0 CA B:ASP181 4.9 18.4 1.0 CE B:LYS13 5.0 37.1 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