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

The structure of O-Methyltransferase From Lycoris Longituba Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde, PDB code: 8xdp 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)	47.90 / 1.75
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.781, 81.421, 118.454, 90, 90, 90
R / Rfree (%)	15.8 / 18.9

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

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Longituba 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 Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:21.4 occ:1.00 OD2 A:ASP181 2.0 23.9 1.0 O A:HOH712 2.1 21.9 1.0 O A:HOH825 2.1 27.7 1.0 OD1 A:ASN182 2.1 21.7 1.0 O A:HOH791 2.2 28.5 1.0 OD1 A:ASP155 2.2 21.4 1.0 CG A:ASP155 3.0 24.4 1.0 CG A:ASP181 3.1 21.8 1.0 CG A:ASN182 3.1 21.3 1.0 OD2 A:ASP155 3.2 19.7 1.0 ND2 A:ASN182 3.4 21.4 1.0 CB A:ASP181 3.6 17.0 1.0 NZ A:LYS158 3.9 31.8 1.0 OD1 A:ASP181 4.1 25.2 1.0 O A:ALA53 4.1 21.7 1.0 O A:HOH870 4.2 39.3 1.0 O A:HOH742 4.3 26.5 1.0 O A:HOH804 4.4 23.9 1.0 CB A:ASP155 4.4 19.7 1.0 CB A:ASN182 4.5 20.9 1.0 N A:ASN182 4.7 15.7 1.0 O A:HOH719 4.7 28.2 1.0 C A:ASP181 4.8 16.2 1.0 CA A:ASP181 4.8 15.8 1.0 CE A:LYS158 4.9 27.5 1.0 O A:ASP155 4.9 26.4 1.0 CG2 A:VAL55 4.9 19.8 1.0 CA A:ASP155 5.0 18.4 1.0 CA A:VAL55 5.0 17.7 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba 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 Complexed with Mg, Sah, and 3,4-Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:22.8 occ:1.00 OD2 B:ASP181 1.9 29.5 1.0 OD1 B:ASP155 2.1 21.0 1.0 O B:HOH621 2.1 21.3 1.0 OD1 B:ASN182 2.1 21.8 1.0 O4 B:H6N501 2.2 37.0 0.4 O4 B:H6N501 2.2 41.3 0.6 O3 B:H6N501 2.4 41.9 0.4 O B:HOH601 2.5 41.2 1.0 O3 B:H6N501 2.5 39.9 0.6 CG B:ASP155 3.0 23.5 1.0 CG B:ASP181 3.0 27.0 1.0 C4 B:H6N501 3.1 40.4 0.4 CG B:ASN182 3.1 25.0 1.0 C4 B:H6N501 3.1 41.2 0.6 C3 B:H6N501 3.2 41.3 0.4 OD2 B:ASP155 3.2 20.1 1.0 C3 B:H6N501 3.2 40.8 0.6 ND2 B:ASN182 3.4 22.2 1.0 CB B:ASP181 3.6 16.4 1.0 NZ B:LYS158 4.0 29.7 1.0 OD1 B:ASP181 4.0 31.3 1.0 O B:ALA53 4.2 22.2 1.0 O B:HOH630 4.3 30.3 1.0 C5 B:H6N501 4.4 41.1 0.4 CB B:ASP155 4.4 19.4 1.0 O B:HOH723 4.4 34.1 1.0 C5 B:H6N501 4.4 41.2 0.6 CB B:ASN182 4.5 19.7 1.0 C2 B:H6N501 4.5 41.4 0.4 C2 B:H6N501 4.6 42.0 0.6 C B:ASP181 4.7 16.9 1.0 N B:ASN182 4.8 17.4 1.0 CA B:ASP181 4.8 15.5 1.0 CE B:LYS158 4.8 29.1 1.0 O B:HOH602 4.8 39.8 1.0 CA B:ASP155 4.9 18.4 1.0 O B:ASP155 4.9 26.6 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