Magnesium in PDB 8xdy: O-Methyltransferase From Lycoris Longituba M52A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde

The structure of O-Methyltransferase From Lycoris Longituba M52A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde, PDB code: 8xdy 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)	47.76 / 2.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.857, 81.492, 117.872, 90, 90, 90
R / Rfree (%)	17.8 / 20.1

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Longituba M52A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde (pdb code 8xdy). 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 Longituba M52A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde, PDB code: 8xdy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Longituba M52A Variant 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 Longituba M52A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:22.6 occ:1.00 OD2 A:ASP181 1.9 34.4 1.0 O A:HOH406 2.1 24.0 1.0 OD1 A:ASP155 2.2 34.4 1.0 OD1 A:ASN182 2.2 26.0 1.0 O A:HOH483 2.3 31.9 1.0 O A:HOH460 2.6 39.1 1.0 CG A:ASP155 2.9 32.3 1.0 CG A:ASP181 3.0 32.2 1.0 OD2 A:ASP155 3.0 32.1 1.0 CG A:ASN182 3.2 25.7 1.0 ND2 A:ASN182 3.4 24.2 1.0 CB A:ASP181 3.6 29.2 1.0 NZ A:LYS158 3.9 33.3 1.0 OD1 A:ASP181 4.0 33.2 1.0 O A:ALA53 4.1 27.4 1.0 CB A:ASP155 4.4 30.9 1.0 O A:HOH432 4.4 23.6 1.0 O A:HOH425 4.4 34.5 1.0 CB A:ASN182 4.6 25.7 1.0 O A:HOH521 4.7 47.0 1.0 N A:ASN182 4.8 25.1 1.0 O A:HOH404 4.8 34.3 1.0 C A:ASP181 4.8 26.4 1.0 CA A:ASP181 4.8 27.9 1.0 CG2 A:VAL55 4.9 23.6 1.0 CA A:ASP155 4.9 29.4 1.0 CE A:LYS158 5.0 33.5 1.0 O A:ASP155 5.0 29.3 1.0 CA A:VAL55 5.0 24.5 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba M52A Variant 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 Longituba M52A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:24.3 occ:1.00 O3 B:H6N503 2.1 26.7 0.4 O4 B:H6N503 2.1 26.8 0.6 OD1 B:ASP155 2.1 35.2 1.0 OD2 B:ASP181 2.2 35.5 1.0 O3 B:H6N503 2.2 27.2 0.6 OD1 B:ASN182 2.2 26.3 1.0 O B:HOH632 2.2 24.0 1.0 O4 B:H6N503 2.3 28.2 0.4 C4 B:H6N503 2.9 27.8 0.6 C3 B:H6N503 2.9 27.8 0.4 C3 B:H6N503 3.0 28.5 0.6 C4 B:H6N503 3.0 28.4 0.4 CG B:ASP155 3.1 31.9 1.0 CG B:ASN182 3.1 25.3 1.0 CG B:ASP181 3.3 32.3 1.0 OD2 B:ASP155 3.3 32.0 1.0 ND2 B:ASN182 3.3 25.4 1.0 NZ B:LYS158 3.4 26.3 1.0 CB B:ASP181 3.9 28.3 1.0 O B:ALA53 4.1 30.5 1.0 O B:HOH654 4.1 24.6 1.0 NZ B:LYS13 4.1 32.2 1.0 C5 B:H6N503 4.3 28.0 0.6 C2 B:H6N503 4.3 28.0 0.4 OD1 B:ASP181 4.3 33.0 1.0 C2 B:H6N503 4.3 29.4 0.6 CE B:LYS158 4.3 26.4 1.0 C5 B:H6N503 4.4 29.5 0.4 CB B:ASP155 4.5 28.2 1.0 CB B:ASN182 4.5 23.6 1.0 O B:ASP155 4.7 26.2 1.0 CA B:ASP155 4.8 26.5 1.0 C B:ASP181 4.9 25.4 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