Magnesium in PDB 8xe5: Norbelladine 4'-O-Methyltransferase Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde

The structure of Norbelladine 4'-O-Methyltransferase Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde, PDB code: 8xe5 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)	45.54 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.328, 79.901, 91.286, 90, 93.86, 90
R / Rfree (%)	19.1 / 22.5

The binding sites of Magnesium atom in the Norbelladine 4'-O-Methyltransferase Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde (pdb code 8xe5). 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 Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde, PDB code: 8xe5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Norbelladine 4'-O-Methyltransferase Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde


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 Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:19.3 occ:1.00 OD2 A:ASP181 2.0 15.9 1.0 O4 A:H6N303 2.0 51.3 0.3 O A:HOH408 2.0 39.5 1.0 O3 A:H6N303 2.1 51.2 0.7 OD1 A:ASP155 2.3 13.5 1.0 OD1 A:ASN182 2.3 14.5 1.0 O4 A:H6N303 2.4 51.8 0.7 O3 A:H6N303 2.6 51.8 0.3 OD2 A:ASP155 2.8 17.5 1.0 CG A:ASP155 2.8 15.4 1.0 C3 A:H6N303 3.0 51.6 0.7 C4 A:H6N303 3.0 51.6 0.3 CG A:ASP181 3.1 14.1 1.0 C4 A:H6N303 3.1 51.6 0.7 C3 A:H6N303 3.2 51.7 0.3 CG A:ASN182 3.4 14.3 1.0 CB A:ASP181 3.7 12.9 1.0 ND2 A:ASN182 3.8 14.4 1.0 NZ A:LYS158 4.0 28.9 1.0 O A:ALA53 4.0 15.2 1.0 OD1 A:ASP181 4.1 15.0 1.0 O A:HOH404 4.2 36.8 1.0 C5 A:H6N303 4.3 51.8 0.3 C2 A:H6N303 4.3 51.8 0.7 CB A:ASP155 4.3 14.9 1.0 CG2 A:VAL55 4.4 15.7 1.0 C5 A:H6N303 4.5 51.8 0.7 C2 A:H6N303 4.6 51.8 0.3 CB A:ASN182 4.6 13.1 1.0 CE A:LYS158 4.7 26.8 1.0 C A:ASP181 4.9 12.9 1.0 N A:ASN182 4.9 13.1 1.0 CA A:ASP181 4.9 13.9 1.0 CB A:SAH302 5.0 15.9 1.0 C A:ALA53 5.0 16.7 1.0 CA A:ASP155 5.0 15.5 1.0

Magnesium binding site 2 out of 4 in the Norbelladine 4'-O-Methyltransferase Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde


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 Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.0 occ:1.00 OD2 B:ASP181 2.1 17.2 1.0 OD1 B:ASP155 2.1 12.0 1.0 O B:HOH602 2.1 31.8 1.0 O B:HOH650 2.1 22.8 1.0 OD1 B:ASN182 2.1 17.8 1.0 OD2 B:ASP155 2.6 14.9 1.0 CG B:ASP155 2.6 13.5 1.0 CG B:ASP181 3.2 15.7 1.0 CG B:ASN182 3.2 17.6 1.0 O B:HOH632 3.6 32.2 1.0 ND2 B:ASN182 3.6 18.1 1.0 NZ B:LYS158 3.7 24.1 1.0 CB B:ASP181 3.7 14.8 1.0 O B:HOH754 3.8 38.7 1.0 O B:ALA53 4.1 16.9 1.0 CB B:ASP155 4.1 12.9 1.0 OD1 B:ASP181 4.2 14.4 1.0 CE B:LYS158 4.5 24.8 1.0 CB B:ASN182 4.5 16.1 1.0 CG2 B:VAL55 4.6 14.7 1.0 CG B:SAH503 4.7 16.6 1.0 CB B:SAH503 4.8 15.7 1.0 CA B:ASP155 4.8 14.3 1.0 C B:ASP181 4.8 13.4 1.0 N B:ASN182 4.9 14.2 1.0 O B:ASP155 4.9 15.8 1.0 CA B:ASP181 4.9 14.0 1.0

Magnesium binding site 3 out of 4 in the Norbelladine 4'-O-Methyltransferase Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde


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 Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:23.6 occ:1.00 O C:HOH437 2.0 24.5 1.0 OD2 C:ASP181 2.1 18.4 1.0 OD1 C:ASP155 2.1 12.5 1.0 OD1 C:ASN182 2.1 18.8 1.0 O3 C:H6N303 2.4 56.0 0.4 O4 C:H6N303 2.4 56.0 0.6 O4 C:H6N303 2.4 56.5 0.4 O3 C:H6N303 2.6 56.6 0.6 OD2 C:ASP155 2.7 12.9 1.0 CG C:ASP155 2.7 12.8 1.0 CG C:ASP181 3.1 17.3 1.0 C3 C:H6N303 3.2 56.2 0.4 C4 C:H6N303 3.3 56.4 0.4 CG C:ASN182 3.3 17.2 1.0 C4 C:H6N303 3.3 56.2 0.6 C3 C:H6N303 3.4 56.4 0.6 CB C:ASP181 3.7 15.6 1.0 O C:HOH467 3.7 37.0 1.0 NZ C:LYS158 3.8 19.2 1.0 ND2 C:ASN182 3.8 15.6 1.0 O C:ALA53 4.2 17.7 1.0 OD1 C:ASP181 4.2 18.1 1.0 CB C:ASP155 4.2 13.0 1.0 O C:HOH406 4.2 40.1 1.0 CE C:LYS158 4.5 18.7 1.0 CB C:ASN182 4.5 16.4 1.0 C2 C:H6N303 4.6 56.3 0.4 C5 C:H6N303 4.6 56.3 0.4 C5 C:H6N303 4.6 56.3 0.6 CG2 C:VAL55 4.7 13.6 1.0 C2 C:H6N303 4.7 56.3 0.6 N C:ASN182 4.8 14.1 1.0 C C:ASP181 4.8 15.9 1.0 CA C:ASP155 4.8 14.8 1.0 CA C:ASP181 4.9 15.7 1.0 CB C:SAH302 4.9 18.5 1.0 CG C:SAH302 5.0 18.7 1.0

Magnesium binding site 4 out of 4 in the Norbelladine 4'-O-Methyltransferase Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde


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 Complexed with Mg, Sah, and 3,4- Dihydroxybenzaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:26.5 occ:1.00 OD1 D:ASN182 2.1 15.1 1.0 OD2 D:ASP181 2.1 18.8 1.0 O D:HOH414 2.1 22.9 1.0 OD1 D:ASP155 2.2 15.3 1.0 O D:HOH492 2.3 42.1 1.0 O D:HOH523 2.4 35.5 1.0 OD2 D:ASP155 2.8 13.8 1.0 CG D:ASP155 2.8 14.7 1.0 CG D:ASN182 3.1 15.5 1.0 CG D:ASP181 3.2 16.4 1.0 ND2 D:ASN182 3.5 16.9 1.0 O D:HOH439 3.7 32.5 1.0 CB D:ASP181 3.8 13.1 1.0 NZ D:LYS158 3.8 16.4 1.0 O D:ALA53 4.1 18.2 1.0 OD1 D:ASP181 4.3 16.8 1.0 CB D:ASP155 4.3 14.2 1.0 CB D:ASN182 4.5 13.3 1.0 O D:HOH514 4.5 33.4 1.0 CE D:LYS158 4.6 17.5 1.0 CG2 D:VAL55 4.8 12.7 1.0 N D:ASN182 4.8 11.9 1.0 C D:ASP181 4.8 12.7 1.0 CG D:SAH302 4.9 14.4 1.0 CB D:SAH302 4.9 14.9 1.0 CA D:ASP155 4.9 14.1 1.0 CA D:ASP181 5.0 12.1 1.0 O D:ASP155 5.0 14.7 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