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

The structure of O-Methyltransferase From Lycoris Longituba M52S Variant Complexed with Mg and Sah, PDB code: 8xdu 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)	48.54 / 1.92
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.529, 81.208, 121.11, 90, 90, 90
R / Rfree (%)	15.4 / 19.8

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

Magnesium binding site 1 out of 2 in the O-Methyltransferase From Lycoris Longituba M52S 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 Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.9 occ:1.00 OD2 A:ASP181 2.0 11.3 1.0 OD1 A:ASN182 2.1 12.9 1.0 O A:HOH691 2.1 21.5 1.0 O A:HOH766 2.2 20.2 1.0 O A:HOH639 2.2 11.7 1.0 OD1 A:ASP155 2.2 12.0 1.0 CG A:ASP155 3.0 13.6 1.0 CG A:ASN182 3.1 14.6 1.0 CG A:ASP181 3.1 11.2 1.0 OD2 A:ASP155 3.2 13.3 1.0 ND2 A:ASN182 3.4 15.3 1.0 CB A:ASP181 3.6 8.5 1.0 NZ A:LYS158 3.9 16.3 1.0 O A:ALA53 4.1 12.7 1.0 OD1 A:ASP181 4.1 13.8 1.0 O A:HOH807 4.4 22.2 1.0 CE A:LYS158 4.4 16.3 1.0 O A:HOH737 4.4 16.3 1.0 CB A:ASP155 4.4 12.2 1.0 CB A:ASN182 4.4 13.2 1.0 O A:HOH635 4.4 14.5 1.0 N A:ASN182 4.7 8.4 1.0 C A:ASP181 4.8 11.4 1.0 CA A:ASP181 4.8 10.4 1.0 O A:HOH661 4.9 24.6 1.0 O A:ASP155 4.9 18.1 1.0 CA A:VAL55 5.0 14.1 1.0 CA A:ASP155 5.0 11.4 1.0

Magnesium binding site 2 out of 2 in the O-Methyltransferase From Lycoris Longituba M52S 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 Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:13.2 occ:1.00 OD2 B:ASP181 2.0 13.0 1.0 O B:HOH403 2.1 10.1 1.0 OD1 B:ASN182 2.1 13.3 1.0 O B:HOH551 2.1 12.4 1.0 OD1 B:ASP155 2.2 15.0 1.0 O B:HOH511 2.2 14.1 1.0 CG B:ASP155 3.0 13.5 1.0 CG B:ASP181 3.0 12.8 1.0 CG B:ASN182 3.1 14.3 1.0 OD2 B:ASP155 3.1 15.3 1.0 ND2 B:ASN182 3.5 15.6 1.0 CB B:ASP181 3.6 9.4 1.0 NZ B:LYS158 3.9 26.0 1.0 OD1 B:ASP181 4.1 17.0 1.0 O B:ALA53 4.2 9.5 1.0 O B:HOH613 4.3 30.6 1.0 O B:HOH434 4.4 17.9 1.0 CB B:ASP155 4.4 10.4 1.0 CB B:ASN182 4.5 9.8 1.0 O B:HOH519 4.5 16.4 1.0 CE B:LYS158 4.6 24.3 1.0 N B:ASN182 4.8 7.3 1.0 C B:ASP181 4.8 10.0 1.0 O B:HOH413 4.8 19.2 1.0 CA B:ASP181 4.8 7.9 1.0 CA B:VAL55 4.9 10.0 1.0 O B:ASP155 4.9 15.3 1.0 CG2 B:VAL55 4.9 10.8 1.0 CA B:ASP155 5.0 8.4 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