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

The structure of O-Methyltransferase From Lycoris Longituba F186Y Variant Complexed with Mg and Sah, PDB code: 8xds 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)	47.86 / 1.97
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.49, 81.229, 118.468, 90, 90, 90
R / Rfree (%)	16 / 20.2

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

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Longituba 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 F186Y Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.8 occ:1.00 OD2 A:ASP181 2.0 19.8 1.0 O A:HOH610 2.1 15.2 1.0 O A:HOH688 2.1 19.4 1.0 O A:HOH712 2.1 17.2 1.0 OD1 A:ASP155 2.1 18.0 1.0 OD1 A:ASN182 2.2 20.6 1.0 CG A:ASP155 2.9 19.0 1.0 CG A:ASP181 3.0 17.9 1.0 OD2 A:ASP155 3.1 18.9 1.0 CG A:ASN182 3.2 18.8 1.0 CB A:ASP181 3.6 14.0 1.0 ND2 A:ASN182 3.6 17.9 1.0 OD1 A:ASP181 4.1 20.8 1.0 NZ A:LYS158 4.1 26.0 1.0 O A:ALA53 4.1 17.2 1.0 O A:HOH783 4.2 28.5 1.0 CB A:ASP155 4.3 20.7 1.0 O A:HOH659 4.4 20.8 1.0 CE A:LYS158 4.4 24.0 1.0 CB A:ASN182 4.5 17.1 1.0 O A:HOH618 4.5 21.5 1.0 N A:ASN182 4.7 15.4 1.0 C A:ASP181 4.8 13.2 1.0 O A:ASP155 4.8 20.8 1.0 CA A:ASP181 4.8 13.9 1.0 O A:HOH632 4.8 22.2 1.0 CG2 A:VAL55 4.8 17.0 1.0 CA A:ASP155 4.9 19.7 1.0 CA A:VAL55 4.9 17.6 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba 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 F186Y Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:17.8 occ:1.00 OD2 B:ASP181 2.0 24.5 1.0 O B:HOH500 2.1 21.5 1.0 OD1 B:ASN182 2.1 18.3 1.0 O B:HOH525 2.1 18.5 1.0 O B:HOH403 2.2 15.7 1.0 OD1 B:ASP155 2.2 16.7 1.0 CG B:ASP155 3.0 18.2 1.0 CG B:ASP181 3.0 22.9 1.0 CG B:ASN182 3.1 16.2 1.0 OD2 B:ASP155 3.1 20.2 1.0 ND2 B:ASN182 3.4 15.3 1.0 CB B:ASP181 3.7 18.2 1.0 NZ B:LYS158 3.9 28.0 1.0 OD1 B:ASP181 4.0 24.1 1.0 O B:ALA53 4.1 18.4 1.0 O B:HOH564 4.2 31.1 1.0 O B:HOH434 4.3 19.9 1.0 O B:HOH505 4.4 17.6 1.0 CB B:ASN182 4.4 13.8 1.0 CB B:ASP155 4.5 16.3 1.0 N B:ASN182 4.7 13.4 1.0 C B:ASP181 4.8 14.9 1.0 O B:HOH422 4.8 25.2 1.0 CA B:ASP181 4.9 15.9 1.0 CE B:LYS158 4.9 27.8 1.0 CA B:VAL55 5.0 17.9 1.0 O B:ASP155 5.0 21.9 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