Magnesium in PDB 8xdt: O-Methyltransferase From Lycoris Longituba M52T Variant Complexed with Mg and Sah

The structure of O-Methyltransferase From Lycoris Longituba M52T Variant Complexed with Mg and Sah, PDB code: 8xdt 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)	49.85 / 2.65
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.854, 81.487, 116.945, 90, 90, 90
R / Rfree (%)	17.6 / 22

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Longituba M52T Variant Complexed with Mg and Sah (pdb code 8xdt). 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 M52T Variant Complexed with Mg and Sah, PDB code: 8xdt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Longituba M52T 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 M52T Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:13.6 occ:1.00 OD2 A:ASP181 2.0 23.1 1.0 O A:HOH440 2.1 21.2 1.0 O A:HOH415 2.2 34.8 1.0 O A:HOH401 2.2 31.3 1.0 OD1 A:ASN182 2.3 28.4 1.0 OD1 A:ASP155 2.6 34.2 1.0 OD2 A:ASP155 3.1 31.8 1.0 CG A:ASP181 3.1 27.9 1.0 CG A:ASP155 3.2 31.2 1.0 CG A:ASN182 3.3 27.4 1.0 ND2 A:ASN182 3.5 26.9 1.0 CB A:ASP181 3.9 24.6 1.0 O A:HOH407 3.9 19.1 1.0 OD1 A:ASP181 3.9 32.9 1.0 O A:ALA53 3.9 18.9 1.0 NZ A:LYS158 4.2 30.5 1.0 O A:HOH451 4.3 33.1 1.0 O A:HOH428 4.5 37.8 1.0 CE A:LYS158 4.6 27.6 1.0 CB A:ASN182 4.7 24.7 1.0 CB A:ASP155 4.7 26.6 1.0 CG2 A:VAL55 4.7 22.1 1.0 CA A:VAL55 4.8 24.6 1.0 N A:ASN182 4.9 22.7 1.0 CB A:VAL55 4.9 23.8 1.0 C A:ALA53 4.9 15.8 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba M52T 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 M52T Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:33.8 occ:1.00 OD2 B:ASP181 2.2 17.8 1.0 O B:HOH403 2.2 44.1 1.0 O B:HOH437 2.2 33.0 1.0 O B:HOH408 2.2 49.2 1.0 OD1 B:ASN182 2.3 30.5 1.0 OD1 B:ASP155 2.4 36.8 1.0 CG B:ASP155 3.1 33.3 1.0 OD2 B:ASP155 3.1 34.4 1.0 CG B:ASP181 3.3 24.8 1.0 CG B:ASN182 3.3 27.0 1.0 O B:HOH432 3.4 27.1 1.0 ND2 B:ASN182 3.5 25.2 1.0 NZ B:LYS158 3.8 31.3 1.0 O B:ALA53 3.8 35.0 1.0 CB B:ASP181 4.0 25.3 1.0 OD1 B:ASP181 4.2 28.0 1.0 O B:HOH415 4.5 29.6 1.0 CB B:ASP155 4.6 25.6 1.0 CB B:ASN182 4.7 28.2 1.0 C B:ALA53 4.8 33.3 1.0 CE B:LYS158 4.8 32.4 1.0 CA B:VAL55 4.9 20.9 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