Magnesium in PDB 8xe0: O-Methyltransferase From Lycoris Longituba M52W Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde

The structure of O-Methyltransferase From Lycoris Longituba M52W Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde, PDB code: 8xe0 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)	47.29 / 2.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.421, 80.862, 116.597, 90, 90, 90
R / Rfree (%)	20.3 / 23.3

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Longituba M52W Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde (pdb code 8xe0). 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 M52W Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde, PDB code: 8xe0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Longituba M52W 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 M52W Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.8 occ:1.00 OD2 A:ASP181 1.9 47.2 1.0 O A:HOH607 2.1 47.8 1.0 OD1 A:ASN182 2.1 43.0 1.0 OD1 A:ASP155 2.2 37.3 1.0 O4 A:H6N501 2.4 80.1 1.0 O3 A:H6N501 2.7 75.2 1.0 CG A:ASP155 3.0 38.9 1.0 CG A:ASP181 3.0 47.9 1.0 OD2 A:ASP155 3.1 36.5 1.0 CG A:ASN182 3.2 37.1 1.0 C4 A:H6N501 3.4 81.9 1.0 C3 A:H6N501 3.5 83.0 1.0 ND2 A:ASN182 3.6 33.1 1.0 NZ A:LYS13 3.7 34.0 0.5 CB A:ASP181 3.7 40.2 1.0 NZ A:LYS158 3.8 67.5 1.0 OD1 A:ASP181 3.9 61.1 1.0 O A:ALA53 4.1 40.5 1.0 CB A:ASP155 4.4 32.9 1.0 CE A:LYS158 4.4 62.2 1.0 CB A:ASN182 4.5 34.7 1.0 C5 A:H6N501 4.7 78.0 1.0 N A:ASN182 4.8 35.7 1.0 C A:ASP181 4.8 35.1 1.0 O A:ASP155 4.8 48.2 1.0 CE A:LYS13 4.9 35.9 0.5 C2 A:H6N501 4.9 82.1 1.0 CA A:ASP181 4.9 39.2 1.0 CA A:ASP155 4.9 36.2 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba M52W 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 M52W Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:56.0 occ:1.00 O B:HOH404 2.1 46.3 1.0 OD2 B:ASP181 2.2 50.3 1.0 O B:HOH405 2.4 62.2 1.0 OD1 B:ASP155 2.4 40.7 1.0 O B:HOH440 2.4 67.7 1.0 OD1 B:ASN182 2.4 38.1 1.0 CG B:ASP155 3.1 41.5 1.0 OD2 B:ASP155 3.1 37.0 1.0 CG B:ASN182 3.2 42.8 1.0 CG B:ASP181 3.2 50.9 1.0 ND2 B:ASN182 3.3 41.9 1.0 O B:ALA53 3.8 48.2 1.0 NZ B:LYS158 3.8 48.3 1.0 CB B:ASP181 4.0 43.7 1.0 OD1 B:ASP181 4.2 57.5 1.0 CB B:ASP155 4.6 41.1 1.0 CB B:ASN182 4.7 36.6 1.0 C B:ALA53 4.8 47.7 1.0 O B:ASP155 4.8 49.5 1.0 CE B:LYS158 4.8 47.4 1.0 CB B:SAH302 4.9 48.7 1.0 CA B:VAL55 4.9 49.8 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