Magnesium in PDB 8xe2: O-Methyltransferase From Lycoris Longituba D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde

The structure of O-Methyltransferase From Lycoris Longituba D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde, PDB code: 8xe2 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 / 2.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.514, 81.596, 116.427, 90, 91.37, 90
R / Rfree (%)	20.7 / 24

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Longituba D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde (pdb code 8xe2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the O-Methyltransferase From Lycoris Longituba D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde, PDB code: 8xe2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the O-Methyltransferase From Lycoris Longituba D230A 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 D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:37.6 occ:1.00 O4 A:H6N605 2.0 38.2 1.0 O A:HOH707 2.0 32.2 1.0 OD2 A:ASP181 2.1 28.4 1.0 O3 A:H6N605 2.1 39.1 1.0 OD1 A:ASN182 2.3 36.3 1.0 OD1 A:ASP155 2.4 36.6 1.0 C4 A:H6N605 2.8 38.1 1.0 C3 A:H6N605 2.8 38.6 1.0 CG A:ASP181 3.1 28.6 1.0 CG A:ASN182 3.2 35.0 1.0 CG A:ASP155 3.3 33.8 1.0 OD2 A:ASP155 3.4 32.2 1.0 ND2 A:ASN182 3.5 36.0 1.0 NZ A:LYS158 3.9 20.2 1.0 CB A:ASP181 3.9 28.3 1.0 OD1 A:ASP181 4.0 27.0 1.0 NZ A:LYS13 4.0 43.5 1.0 O A:ALA53 4.1 33.0 1.0 C5 A:H6N605 4.1 37.7 1.0 C2 A:H6N605 4.2 38.3 1.0 O A:HOH711 4.2 41.0 1.0 CE A:LYS158 4.5 20.9 1.0 CB A:ASN182 4.6 32.3 1.0 CB A:ASP155 4.7 32.2 1.0 C A:ALA53 5.0 31.6 1.0 C A:ASP181 5.0 30.1 1.0 N A:ASN182 5.0 30.7 1.0 O A:ASP155 5.0 30.3 1.0

Magnesium binding site 2 out of 4 in the O-Methyltransferase From Lycoris Longituba D230A 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 D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:35.9 occ:1.00 O B:HOH401 2.0 34.6 1.0 O4 B:H6N303 2.1 30.2 1.0 O3 B:H6N303 2.2 30.5 1.0 OD1 B:ASP155 2.2 35.2 1.0 OD2 B:ASP181 2.2 35.0 1.0 OD1 B:ASN182 2.2 36.5 1.0 OD2 B:ASP155 2.8 33.0 1.0 CG B:ASP155 2.8 34.0 1.0 C4 B:H6N303 2.9 30.8 1.0 C3 B:H6N303 2.9 31.3 1.0 CG B:ASP181 3.2 34.5 1.0 CG B:ASN182 3.3 37.2 1.0 NZ B:LYS158 3.7 26.8 1.0 ND2 B:ASN182 3.8 37.2 1.0 CB B:ASP181 3.9 33.5 1.0 OD1 B:ASP181 4.1 34.2 1.0 O B:ALA53 4.1 31.6 1.0 NZ B:LYS13 4.2 38.3 1.0 C5 B:H6N303 4.2 31.6 1.0 C2 B:H6N303 4.3 31.6 1.0 CB B:ASP155 4.3 33.6 1.0 CE B:LYS158 4.4 27.6 1.0 CB B:ASN182 4.6 37.7 1.0 O B:ASP155 4.9 34.5 1.0 CA B:ASP155 4.9 32.3 1.0 C B:ASP181 5.0 33.2 1.0

Magnesium binding site 3 out of 4 in the O-Methyltransferase From Lycoris Longituba D230A 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 3 of O-Methyltransferase From Lycoris Longituba D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:34.4 occ:1.00 O C:HOH428 2.0 24.2 1.0 OD2 C:ASP181 2.1 40.7 1.0 O C:HOH447 2.2 46.9 1.0 OD1 C:ASP155 2.4 36.5 1.0 OD1 C:ASN182 2.5 35.0 1.0 CG C:ASP155 3.2 34.4 1.0 OD2 C:ASP155 3.2 35.1 1.0 CG C:ASP181 3.3 40.2 1.0 CG C:ASN182 3.5 34.1 1.0 ND2 C:ASN182 3.7 33.8 1.0 O C:ALA53 3.9 41.5 1.0 CB C:ASP181 4.0 37.6 1.0 O C:HOH413 4.1 44.1 1.0 NZ C:LYS158 4.1 35.1 1.0 OD1 C:ASP181 4.2 40.8 1.0 CB C:ASP155 4.7 30.7 1.0 CE C:LYS158 4.7 35.8 1.0 O C:HOH455 4.7 30.7 1.0 C C:ALA53 4.8 40.7 1.0 CB C:ASN182 4.9 32.8 1.0 CA C:VAL55 4.9 33.3 1.0 O C:ASP155 4.9 31.3 1.0

Magnesium binding site 4 out of 4 in the O-Methyltransferase From Lycoris Longituba D230A 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 4 of O-Methyltransferase From Lycoris Longituba D230A Variant Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:43.6 occ:1.00 OD2 D:ASP181 2.1 40.7 1.0 O D:HOH407 2.1 52.1 1.0 OD1 D:ASP155 2.4 41.4 1.0 O D:HOH404 2.4 31.5 1.0 OD1 D:ASN182 2.6 36.8 1.0 OD2 D:ASP155 3.0 39.5 1.0 CG D:ASP155 3.0 39.7 1.0 CG D:ASP181 3.3 38.2 1.0 CG D:ASN182 3.6 36.2 1.0 O D:ALA53 3.9 42.5 1.0 ND2 D:ASN182 3.9 36.7 1.0 NZ D:LYS158 4.0 28.2 1.0 O D:HOH421 4.0 34.1 1.0 CB D:ASP181 4.0 36.5 1.0 OD1 D:ASP181 4.2 35.9 1.0 CB D:ASP155 4.5 38.5 1.0 CE D:LYS158 4.6 28.4 1.0 C D:ALA53 4.8 41.8 1.0 CG D:SAH302 4.9 38.1 1.0 CB D:ASN182 4.9 34.4 1.0 CB D:SAH302 4.9 38.6 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