Magnesium in PDB 8z8r: Norbelladine 4'-O-Methyltransferase S52T Complexed with Mg and Sah

All present enzymatic activity of Norbelladine 4'-O-Methyltransferase S52T Complexed with Mg and Sah:
2.1.1.336;

The structure of Norbelladine 4'-O-Methyltransferase S52T Complexed with Mg and Sah, PDB code: 8z8r 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)	45.65 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.352, 79.723, 91.517, 90, 94.01, 90
R / Rfree (%)	15.8 / 18.9

The binding sites of Magnesium atom in the Norbelladine 4'-O-Methyltransferase S52T Complexed with Mg and Sah (pdb code 8z8r). 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 S52T Complexed with Mg and Sah, PDB code: 8z8r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Norbelladine 4'-O-Methyltransferase S52T 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 S52T Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.0 occ:1.00 OD1 A:ASP155 2.0 15.2 1.0 O A:HOH661 2.0 14.3 1.0 OD2 A:ASP181 2.0 17.1 1.0 OD1 A:ASN182 2.1 15.5 1.0 O A:HOH701 2.2 16.8 1.0 OD2 A:ASP155 2.3 12.4 1.0 CG A:ASP155 2.4 12.5 1.0 CG A:ASP181 3.1 15.5 1.0 CG A:ASN182 3.1 19.0 1.0 ND2 A:ASN182 3.5 24.3 1.0 CB A:ASP181 3.6 11.9 1.0 O A:HOH785 3.9 27.3 1.0 CB A:ASP155 3.9 11.0 1.0 O A:HOH758 3.9 19.1 1.0 O A:ALA53 4.1 14.6 1.0 NZ A:LYS158 4.1 18.2 1.0 OD1 A:ASP181 4.2 15.5 1.0 CE A:LYS158 4.3 20.2 1.0 CG2 A:VAL55 4.4 11.7 1.0 CB A:ASN182 4.5 14.9 1.0 CB A:SAH503 4.5 9.5 1.0 CA A:ASP155 4.6 11.4 1.0 O A:ASP155 4.7 16.3 1.0 C A:ASP181 4.7 9.1 1.0 CG A:SAH503 4.7 12.2 1.0 O A:HOH711 4.7 36.7 1.0 CA A:ASP181 4.8 8.9 1.0 N A:ASN182 4.8 7.2 1.0 N A:SAH503 5.0 9.3 1.0 O A:ASP181 5.0 11.6 1.0

Magnesium binding site 2 out of 4 in the Norbelladine 4'-O-Methyltransferase S52T 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 S52T Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:12.2 occ:1.00 OD2 B:ASP181 2.0 12.8 1.0 OD1 B:ASP155 2.0 12.4 1.0 OD1 B:ASN182 2.0 14.1 1.0 O B:HOH662 2.1 15.1 1.0 O B:HOH755 2.2 14.7 1.0 OD2 B:ASP155 2.2 14.1 1.0 CG B:ASP155 2.4 12.6 1.0 CG B:ASN182 3.0 14.5 1.0 CG B:ASP181 3.1 11.4 1.0 ND2 B:ASN182 3.4 15.0 1.0 CB B:ASP181 3.6 9.6 1.0 CB B:ASP155 3.9 10.2 1.0 NZ B:LYS158 3.9 19.1 1.0 O B:HOH781 4.0 15.9 1.0 O B:HOH822 4.1 19.2 1.0 OD1 B:ASP181 4.1 11.5 1.0 O B:ALA53 4.1 10.0 1.0 CG2 B:VAL55 4.3 8.6 1.0 CB B:ASN182 4.4 11.5 1.0 CE B:LYS158 4.5 22.0 1.0 CB B:SAH503 4.5 12.7 1.0 C B:ASP181 4.6 10.5 1.0 CA B:ASP155 4.7 12.7 1.0 O B:ASP155 4.7 12.6 1.0 CG B:SAH503 4.7 11.7 1.0 N B:ASN182 4.8 10.3 1.0 CA B:ASP181 4.8 11.1 1.0 O B:ASP181 4.8 11.2 1.0 N B:SAH503 4.9 11.8 1.0 OH B:TYR161 4.9 11.1 1.0 O B:HOH663 5.0 36.9 1.0

Magnesium binding site 3 out of 4 in the Norbelladine 4'-O-Methyltransferase S52T 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 S52T Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:17.9 occ:1.00 O C:HOH453 1.9 20.0 1.0 OD2 C:ASP181 2.0 17.0 1.0 OD1 C:ASN182 2.1 16.0 1.0 OD1 C:ASP155 2.1 18.0 1.0 O C:HOH541 2.2 19.6 1.0 O C:HOH449 2.5 35.3 1.0 CG C:ASP155 2.9 16.3 1.0 OD2 C:ASP155 3.0 16.1 1.0 CG C:ASN182 3.1 14.8 1.0 CG C:ASP181 3.1 14.3 1.0 ND2 C:ASN182 3.5 14.9 1.0 CB C:ASP181 3.7 10.9 1.0 CE C:LYS158 4.0 24.0 1.0 O C:ALA53 4.0 13.3 1.0 O C:HOH575 4.0 30.2 1.0 OD1 C:ASP181 4.1 13.6 1.0 NZ C:LYS158 4.2 28.5 1.0 CB C:ASP155 4.3 13.1 1.0 CB C:ASN182 4.4 12.0 1.0 O C:HOH469 4.4 35.2 1.0 CG2 C:VAL55 4.5 16.4 1.0 C C:ASP181 4.7 11.0 1.0 N C:ASN182 4.7 10.8 1.0 CA C:ASP181 4.8 10.9 1.0 CA C:ASP155 5.0 12.5 1.0

Magnesium binding site 4 out of 4 in the Norbelladine 4'-O-Methyltransferase S52T 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 S52T Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:16.1 occ:1.00 OD1 D:ASP155 1.9 16.7 1.0 OD1 D:ASN182 2.0 16.7 1.0 O D:HOH449 2.0 14.3 1.0 OD2 D:ASP181 2.1 15.6 1.0 O D:HOH490 2.2 16.8 1.0 OD2 D:ASP155 2.4 14.6 1.0 CG D:ASP155 2.4 14.8 1.0 CG D:ASP181 3.1 13.8 1.0 CG D:ASN182 3.2 20.2 1.0 CB D:ASP181 3.6 13.4 1.0 ND2 D:ASN182 3.8 26.2 1.0 O D:HOH525 3.9 21.4 1.0 CB D:ASP155 3.9 13.2 1.0 O D:HOH575 4.0 22.4 1.0 O D:ALA53 4.1 17.1 1.0 CE D:LYS158 4.1 15.8 1.0 OD1 D:ASP181 4.2 15.6 1.0 NZ D:LYS158 4.2 18.0 1.0 CG2 D:VAL55 4.4 12.3 1.0 CB D:ASN182 4.4 14.8 1.0 O D:HOH561 4.4 41.2 1.0 CB D:SAH302 4.6 10.7 1.0 CA D:ASP155 4.6 14.5 1.0 C D:ASP181 4.6 12.9 1.0 O D:ASP155 4.7 17.5 1.0 N D:ASN182 4.8 11.0 1.0 CA D:ASP181 4.8 11.5 1.0 CG D:SAH302 4.8 13.6 1.0 O D:ASP181 4.9 11.6 1.0 OH D:TYR161 4.9 12.1 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