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

The structure of O-Methyltransferase From Lycoris Longituba Complexed with Mg and Sah, PDB code: 8xdo 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)	47.73 / 1.37
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.637, 81.183, 118.027, 90, 90, 90
R / Rfree (%)	14.5 / 16.8

The binding sites of Magnesium atom in the O-Methyltransferase From Lycoris Longituba Complexed with Mg and Sah (pdb code 8xdo). 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 and Sah, PDB code: 8xdo:
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 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 Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:11.1 occ:1.00 OD2 A:ASP181 2.0 12.5 1.0 O A:HOH616 2.1 12.4 1.0 O A:HOH798 2.1 14.0 1.0 OD1 A:ASN182 2.1 12.1 1.0 OD1 A:ASP155 2.1 11.7 1.0 O A:HOH761 2.1 14.3 1.0 CG A:ASP155 3.0 12.6 1.0 CG A:ASP181 3.1 12.6 1.0 CG A:ASN182 3.1 10.4 1.0 OD2 A:ASP155 3.3 12.5 1.0 ND2 A:ASN182 3.5 13.5 1.0 CB A:ASP181 3.6 10.2 1.0 NZ A:LYS158 3.9 22.8 1.0 O A:ALA53 4.0 12.1 1.0 OD1 A:ASP181 4.1 14.0 1.0 O A:HOH865 4.3 23.9 1.0 O A:HOH639 4.4 14.7 1.0 CB A:ASP155 4.4 12.1 1.0 O A:HOH698 4.4 13.7 1.0 CB A:ASN182 4.5 9.9 1.0 O A:HOH707 4.8 14.4 1.0 N A:ASN182 4.8 9.1 1.0 C A:ASP181 4.8 9.9 1.0 CA A:ASP181 4.8 8.7 1.0 CA A:VAL55 5.0 9.8 1.0 CA A:ASP155 5.0 11.3 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba 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 Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:11.5 occ:1.00 OD2 B:ASP181 2.0 12.9 1.0 O B:HOH420 2.1 12.4 1.0 O B:HOH582 2.1 15.5 1.0 O B:HOH535 2.1 14.1 1.0 OD1 B:ASP155 2.1 12.2 1.0 OD1 B:ASN182 2.1 11.4 1.0 CG B:ASP155 3.0 11.8 1.0 CG B:ASP181 3.1 14.1 1.0 CG B:ASN182 3.1 10.6 1.0 OD2 B:ASP155 3.3 12.4 1.0 ND2 B:ASN182 3.5 14.0 1.0 CB B:ASP181 3.6 10.3 1.0 O B:HOH408 4.0 50.5 1.0 NZ B:LYS158 4.0 24.0 1.0 O B:ALA53 4.0 12.1 1.0 OD1 B:ASP181 4.1 15.2 1.0 O B:HOH637 4.2 30.0 1.0 O B:HOH446 4.4 14.7 1.0 O B:HOH540 4.4 14.7 1.0 CB B:ASP155 4.4 10.8 1.0 CB B:ASN182 4.5 10.7 1.0 N B:ASN182 4.7 9.4 1.0 C B:ASP181 4.8 8.9 1.0 O B:HOH494 4.8 16.1 1.0 CA B:ASP181 4.9 9.1 1.0 CA B:VAL55 4.9 11.1 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