Magnesium in PDB 8xdv: O-Methyltransferase From Lycoris Longituba M52S-F186Y Variant Complexed with Mg and Sah

The structure of O-Methyltransferase From Lycoris Longituba M52S-F186Y Variant Complexed with Mg and Sah, PDB code: 8xdv 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)	47.16 / 2.32
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.951, 80.894, 116.107, 90, 90, 90
R / Rfree (%)	21.6 / 24.2

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Longituba M52S-F186Y Variant Complexed with Mg and Sah (pdb code 8xdv). 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 M52S-F186Y Variant Complexed with Mg and Sah, PDB code: 8xdv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Longituba M52S-F186Y Variant Complexed with Mg and Sah


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 M52S-F186Y Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:38.5 occ:1.00 OD2 A:ASP181 2.1 38.7 1.0 O A:HOH402 2.1 40.4 1.0 O A:HOH437 2.1 59.4 1.0 OD1 A:ASP155 2.2 42.4 1.0 OD1 A:ASN182 2.2 38.4 1.0 O A:HOH423 2.3 34.0 1.0 CG A:ASP155 3.0 42.2 1.0 OD2 A:ASP155 3.0 41.5 1.0 CG A:ASP181 3.0 38.6 1.0 CG A:ASN182 3.2 37.5 1.0 ND2 A:ASN182 3.5 37.0 1.0 CB A:ASP181 3.7 38.3 1.0 NZ A:LYS158 3.7 48.5 1.0 O A:ALA53 3.9 38.0 1.0 OD1 A:ASP181 4.0 39.0 1.0 O A:HOH415 4.2 48.4 1.0 CB A:ASP155 4.4 42.3 1.0 CB A:ASN182 4.6 37.3 1.0 CE A:LYS158 4.8 48.8 1.0 O A:ASP155 4.8 45.4 1.0 N A:ASN182 4.9 38.0 1.0 C A:ASP181 4.9 38.5 1.0 CA A:ASP181 4.9 38.7 1.0 C A:ALA53 4.9 37.4 1.0 CA A:ASP155 5.0 43.0 1.0 CA A:VAL55 5.0 36.5 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba M52S-F186Y Variant Complexed with Mg and Sah


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 M52S-F186Y Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:60.0 occ:1.00 O B:HOH435 2.0 48.5 1.0 OD2 B:ASP181 2.1 41.9 1.0 O B:HOH415 2.1 42.9 1.0 OD1 B:ASN182 2.2 39.6 1.0 O B:HOH401 2.2 53.7 1.0 OD1 B:ASP155 2.3 43.7 1.0 CG B:ASP155 3.0 42.6 1.0 OD2 B:ASP155 3.1 42.3 1.0 CG B:ASP181 3.1 42.3 1.0 CG B:ASN182 3.1 39.8 1.0 ND2 B:ASN182 3.4 40.0 1.0 CB B:ASP181 3.8 40.5 1.0 NZ B:LYS158 3.9 56.9 1.0 OD1 B:ASP181 4.0 44.3 1.0 O B:ALA53 4.0 42.8 1.0 CB B:ASP155 4.4 41.5 1.0 CB B:ASN182 4.5 39.2 1.0 CE B:LYS158 4.8 56.5 1.0 N B:ASN182 4.8 39.1 1.0 C B:ASP181 4.9 39.6 1.0 CA B:ASP181 5.0 39.4 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