Magnesium in PDB 8z8o: Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah

All present enzymatic activity of Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah:
2.1.1.336;

The structure of Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah, PDB code: 8z8o 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)	45.70 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.416, 79.806, 91.621, 90, 93.95, 90
R / Rfree (%)	15.7 / 18.6

The binding sites of Magnesium atom in the Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah (pdb code 8z8o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah, PDB code: 8z8o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Norbelladine 4'-O-Methyltransferase Y186F 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 Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:20.4 occ:1.00 OD1 A:ASP155 2.0 16.0 1.0 O A:HOH672 2.0 16.9 1.0 OD2 A:ASP181 2.1 16.3 1.0 O A:HOH628 2.1 22.0 1.0 OD1 A:ASN182 2.1 19.8 1.0 OD2 A:ASP155 2.5 12.1 1.0 CG A:ASP155 2.5 15.6 1.0 CG A:ASN182 3.1 26.6 1.0 CG A:ASP181 3.2 15.7 1.0 ND2 A:ASN182 3.5 33.5 1.0 CB A:ASP181 3.7 10.0 1.0 NZ A:LYS158 4.0 17.8 1.0 CB A:ASP155 4.0 11.5 1.0 O A:HOH723 4.0 16.9 1.0 O A:ALA53 4.1 16.6 1.0 OD1 A:ASP181 4.2 14.0 1.0 O A:HOH761 4.3 41.0 1.0 CE A:LYS158 4.3 20.9 1.0 CB A:ASN182 4.5 16.6 1.0 CG2 A:VAL55 4.5 13.6 1.0 CA A:ASP155 4.7 11.7 1.0 CB A:SAH504 4.7 11.5 1.0 C A:ASP181 4.7 10.5 1.0 O A:ASP155 4.8 14.9 1.0 N A:ASN182 4.9 9.7 1.0 CG A:SAH504 4.9 12.6 1.0 CA A:ASP181 4.9 9.1 1.0 O A:ASP181 5.0 12.2 1.0

Magnesium binding site 2 out of 4 in the Norbelladine 4'-O-Methyltransferase Y186F 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 Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:16.7 occ:1.00 OD1 B:ASP155 1.9 15.2 1.0 OD2 B:ASP181 2.0 14.6 1.0 O B:HOH636 2.0 15.2 1.0 OD1 B:ASN182 2.1 15.3 1.0 O B:HOH675 2.2 19.8 1.0 OD2 B:ASP155 2.4 12.9 1.0 CG B:ASP155 2.5 15.2 1.0 CG B:ASN182 3.1 22.1 1.0 CG B:ASP181 3.1 14.9 1.0 ND2 B:ASN182 3.4 26.3 1.0 CB B:ASP181 3.6 9.8 1.0 NZ B:LYS158 3.9 21.5 1.0 O B:HOH753 3.9 18.1 1.0 CB B:ASP155 4.0 10.8 1.0 O B:HOH800 4.0 27.7 1.0 O B:ALA53 4.1 13.5 1.0 OD1 B:ASP181 4.1 11.8 1.0 CB B:ASN182 4.4 17.7 1.0 CG2 B:VAL55 4.4 11.3 1.0 CE B:LYS158 4.5 20.4 1.0 CB B:SAH504 4.6 10.3 1.0 C B:ASP181 4.6 11.3 1.0 O B:HOH752 4.7 46.8 1.0 CA B:ASP155 4.7 10.2 1.0 O B:ASP155 4.7 13.6 1.0 CA B:ASP181 4.8 9.0 1.0 CG B:SAH504 4.8 12.8 1.0 N B:ASN182 4.8 10.3 1.0 O B:ASP181 4.8 12.1 1.0 OH B:TYR161 4.9 12.3 1.0

Magnesium binding site 3 out of 4 in the Norbelladine 4'-O-Methyltransferase Y186F 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 3 of Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:16.4 occ:1.00 O C:HOH429 2.0 20.4 1.0 OD2 C:ASP181 2.0 16.1 1.0 OD1 C:ASP155 2.0 16.0 1.0 OD1 C:ASN182 2.1 16.9 1.0 O C:HOH512 2.1 23.3 1.0 O C:HOH555 2.6 35.1 1.0 CG C:ASP155 2.8 15.5 1.0 OD2 C:ASP155 2.9 14.2 1.0 CG C:ASP181 3.1 15.6 1.0 CG C:ASN182 3.2 15.9 1.0 CB C:ASP181 3.6 10.5 1.0 ND2 C:ASN182 3.7 13.3 1.0 O C:HOH492 4.0 34.3 1.0 CE C:LYS158 4.0 18.8 1.0 O C:ALA53 4.1 16.4 1.0 NZ C:LYS158 4.1 26.3 1.0 OD1 C:ASP181 4.1 13.9 1.0 O C:HOH590 4.1 25.4 1.0 CB C:ASP155 4.2 12.5 1.0 CB C:ASN182 4.5 12.8 1.0 O C:HOH531 4.5 35.9 1.0 CG2 C:VAL55 4.6 13.4 1.0 C C:ASP181 4.7 11.6 1.0 N C:ASN182 4.7 10.4 1.0 CA C:ASP181 4.8 9.8 1.0 CA C:ASP155 4.9 10.6 1.0 O C:ASP155 5.0 14.8 1.0

Magnesium binding site 4 out of 4 in the Norbelladine 4'-O-Methyltransferase Y186F 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 4 of Norbelladine 4'-O-Methyltransferase Y186F Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:17.4 occ:1.00 O D:HOH434 2.0 22.5 1.0 OD1 D:ASP155 2.0 16.1 1.0 OD2 D:ASP181 2.0 16.1 1.0 OD1 D:ASN182 2.1 18.7 1.0 O D:HOH493 2.2 21.2 1.0 CG D:ASP155 2.6 15.1 1.0 OD2 D:ASP155 2.6 14.7 1.0 CG D:ASP181 3.1 15.5 1.0 CG D:ASN182 3.2 20.5 1.0 CB D:ASP181 3.6 11.9 1.0 ND2 D:ASN182 3.8 21.3 1.0 O D:HOH499 3.8 23.4 1.0 CB D:ASP155 4.0 13.2 1.0 O D:ALA53 4.1 16.0 1.0 NZ D:LYS158 4.1 19.5 1.0 CE D:LYS158 4.1 18.2 1.0 OD1 D:ASP181 4.2 14.6 1.0 O D:HOH576 4.3 27.6 1.0 CG2 D:VAL55 4.4 11.8 1.0 CB D:ASN182 4.4 16.1 1.0 O D:HOH557 4.6 41.5 1.0 C D:ASP181 4.7 11.3 1.0 CB D:SAH302 4.7 13.8 1.0 CA D:ASP155 4.7 11.9 1.0 N D:ASN182 4.7 11.3 1.0 CA D:ASP181 4.8 11.5 1.0 O D:ASP155 4.9 16.6 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