Magnesium in PDB 8z8p: Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah

All present enzymatic activity of Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah:
2.1.1.336;

The structure of Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah, PDB code: 8z8p 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)	45.72 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.494, 79.948, 91.634, 90, 93.73, 90
R / Rfree (%)	15.6 / 17.9

The binding sites of Magnesium atom in the Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah (pdb code 8z8p). 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 S52M Variant Complexed with Mg and Sah, PDB code: 8z8p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Norbelladine 4'-O-Methyltransferase S52M 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 Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:20.2 occ:1.00 OD1 A:ASP155 2.0 19.5 1.0 O A:HOH649 2.0 24.2 1.0 OD2 A:ASP181 2.0 16.6 1.0 OD1 A:ASN182 2.1 16.4 1.0 O A:HOH645 2.1 34.6 1.0 O A:HOH699 2.2 23.1 1.0 CG A:ASP155 2.8 13.5 1.0 OD2 A:ASP155 2.9 15.1 1.0 CG A:ASN182 3.1 18.2 1.0 CG A:ASP181 3.1 15.7 1.0 ND2 A:ASN182 3.5 17.4 1.0 CB A:ASP181 3.7 11.9 1.0 NZ A:LYS158 3.8 22.5 1.0 O A:HOH724 3.9 23.9 1.0 O A:ALA53 4.1 15.1 1.0 OD1 A:ASP181 4.2 16.1 1.0 O A:HOH830 4.2 28.2 1.0 CB A:ASP155 4.2 12.9 1.0 O A:HOH713 4.4 35.3 1.0 CB A:ASN182 4.4 14.8 1.0 CG2 A:VAL55 4.6 15.2 1.0 CE A:LYS158 4.6 24.8 1.0 C A:ASP181 4.7 11.4 1.0 N A:ASN182 4.7 9.6 1.0 O A:HOH655 4.8 30.8 1.0 CA A:ASP155 4.8 11.2 1.0 CA A:ASP181 4.8 11.1 1.0 O A:ASP155 4.8 15.6 1.0 CB A:SAH506 4.9 12.4 1.0

Magnesium binding site 2 out of 4 in the Norbelladine 4'-O-Methyltransferase S52M 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 Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:19.1 occ:1.00 OD1 B:ASP155 1.9 19.3 1.0 OD2 B:ASP181 1.9 17.5 1.0 O B:HOH633 2.0 24.8 1.0 OD1 B:ASN182 2.0 19.5 1.0 O B:HOH606 2.1 35.3 1.0 O B:HOH663 2.3 22.3 1.0 CG B:ASP155 2.6 18.4 1.0 OD2 B:ASP155 2.6 17.5 1.0 CG B:ASP181 3.0 14.7 1.0 CG B:ASN182 3.1 20.4 1.0 CB B:ASP181 3.6 12.5 1.0 ND2 B:ASN182 3.6 21.4 1.0 NZ B:LYS158 3.8 20.3 1.0 O B:HOH740 3.9 24.8 1.0 CB B:ASP155 4.1 15.5 1.0 O B:HOH804 4.1 28.6 1.0 OD1 B:ASP181 4.1 16.1 1.0 O B:ALA53 4.1 16.2 1.0 CB B:ASN182 4.4 13.7 1.0 CG2 B:VAL55 4.5 15.3 1.0 O B:HOH658 4.6 39.9 1.0 CE B:LYS158 4.6 26.8 1.0 C B:ASP181 4.6 14.3 1.0 N B:ASN182 4.7 12.9 1.0 CA B:ASP155 4.7 15.4 1.0 CA B:ASP181 4.7 12.8 1.0 O B:ASP155 4.8 15.8 1.0 CB B:SAH503 4.9 15.6 1.0 O B:ASP181 5.0 13.9 1.0 OH B:TYR161 5.0 15.7 1.0

Magnesium binding site 3 out of 4 in the Norbelladine 4'-O-Methyltransferase S52M 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 3 of Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:19.1 occ:1.00 O C:HOH658 1.9 23.0 1.0 OD2 C:ASP181 2.0 17.2 1.0 OD1 C:ASP155 2.1 18.0 1.0 OD1 C:ASN182 2.1 20.5 1.0 O C:HOH721 2.2 25.9 1.0 O C:HOH637 2.5 65.5 1.0 CG C:ASP155 2.8 16.3 1.0 OD2 C:ASP155 2.9 14.6 1.0 CG C:ASP181 3.0 15.2 1.0 CG C:ASN182 3.1 17.9 1.0 CB C:ASP181 3.6 12.7 1.0 ND2 C:ASN182 3.6 18.1 1.0 O C:HOH696 4.0 29.6 1.0 NZ C:LYS158 4.0 24.6 1.0 CE C:LYS158 4.0 21.0 1.0 O C:ALA53 4.1 17.6 1.0 OD1 C:ASP181 4.1 15.1 1.0 CB C:ASP155 4.2 15.1 1.0 O C:HOH786 4.3 30.8 1.0 CB C:ASN182 4.4 14.9 1.0 O C:HOH704 4.4 27.0 1.0 CG2 C:VAL55 4.5 17.2 1.0 C C:ASP181 4.7 14.0 1.0 N C:ASN182 4.7 14.4 1.0 CA C:ASP181 4.8 13.6 1.0 CA C:ASP155 4.9 11.9 1.0 O C:ASP155 4.9 16.4 1.0

Magnesium binding site 4 out of 4 in the Norbelladine 4'-O-Methyltransferase S52M 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 4 of Norbelladine 4'-O-Methyltransferase S52M Variant Complexed with Mg and Sah within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:17.8 occ:1.00 OD1 D:ASN182 2.0 18.4 1.0 OD2 D:ASP181 2.0 18.1 1.0 OD1 D:ASP155 2.0 16.4 1.0 O D:HOH406 2.1 31.2 1.0 O D:HOH464 2.1 23.0 1.0 O D:HOH550 2.3 37.9 1.0 CG D:ASP155 2.7 17.5 1.0 OD2 D:ASP155 2.8 18.0 1.0 CG D:ASN182 3.1 17.8 1.0 CG D:ASP181 3.1 14.5 1.0 ND2 D:ASN182 3.6 20.3 1.0 CB D:ASP181 3.6 13.3 1.0 O D:HOH538 3.9 21.6 1.0 NZ D:LYS158 4.0 18.7 1.0 O D:ALA53 4.1 16.6 1.0 OD1 D:ASP181 4.2 15.1 1.0 CB D:ASP155 4.2 12.8 1.0 CB D:ASN182 4.3 15.9 1.0 O D:HOH629 4.4 26.2 1.0 CE D:LYS158 4.4 19.6 1.0 O D:HOH552 4.5 31.1 1.0 CG2 D:VAL55 4.5 13.1 1.0 C D:ASP181 4.6 15.6 1.0 N D:ASN182 4.7 11.8 1.0 CA D:ASP181 4.8 12.9 1.0 CA D:ASP155 4.8 12.3 1.0 O D:ASP155 4.8 15.7 1.0 CB D:SAH302 4.8 15.8 1.0 O D:HOH578 4.9 28.4 1.0 OH D:TYR161 5.0 12.4 1.0 O D:ASP181 5.0 12.6 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