Magnesium in PDB 4xvy: Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah

All present enzymatic activity of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah:
2.1.1.237;

The structure of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah, PDB code: 4xvy was solved by D.L.Akey, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.73 / 2.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.057, 89.892, 127.655, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.8

The binding sites of Magnesium atom in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah (pdb code 4xvy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah, PDB code: 4xvy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:31.6 occ:1.00 OD1 A:ASP189 2.2 51.3 1.0 O A:HOH405 2.2 44.5 1.0 OD2 A:ASP217 2.3 61.9 1.0 O A:HOH406 2.3 55.7 1.0 O A:HOH404 2.4 33.8 1.0 OD2 A:ASP216 2.4 51.1 1.0 OD1 A:ASP191 2.6 80.5 1.0 CG A:ASP217 3.0 65.5 1.0 OD1 A:ASP217 3.1 69.6 1.0 CG A:ASP189 3.3 50.5 1.0 CG A:ASP216 3.5 51.1 1.0 CG A:ASP191 3.5 76.3 1.0 OD2 A:ASP189 3.8 50.3 1.0 OD2 A:ASP191 3.9 80.4 1.0 CB A:ASP216 4.1 51.0 1.0 NE2 A:GLN246 4.4 54.6 1.0 CB A:ASP217 4.5 61.9 1.0 OD1 A:ASP216 4.5 50.4 1.0 CB A:ASP189 4.6 49.6 1.0 CA A:ASP189 4.7 50.4 1.0 O A:ASP189 4.7 54.3 1.0 C A:ASP189 4.7 53.0 1.0 NH2 A:ARG61 4.8 46.5 1.0 N A:ASP191 4.9 63.7 1.0 CB A:ASP191 4.9 71.7 1.0 C A:ASP216 4.9 54.1 1.0 CG A:SAH302 4.9 36.3 1.0 SD A:SAH302 5.0 45.6 1.0 O A:ASP216 5.0 54.4 1.0

Magnesium binding site 2 out of 2 in the Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycf Mycinamicin III 3'-O-Methyltransferase in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:35.4 occ:1.00 OD1 B:ASP189 2.1 62.5 1.0 OD2 B:ASP216 2.1 49.0 1.0 O B:HOH421 2.3 49.2 1.0 OD1 B:ASP191 2.3 67.9 1.0 O B:HOH423 2.5 42.2 1.0 O B:HOH422 2.6 48.6 1.0 CG B:ASP216 3.2 48.1 1.0 CG B:ASP189 3.2 60.5 1.0 CG B:ASP191 3.3 70.4 1.0 OD2 B:ASP217 3.3 62.2 1.0 OD2 B:ASP191 3.5 72.0 1.0 OD2 B:ASP189 3.7 56.4 1.0 CB B:ASP216 3.8 47.5 1.0 CB B:ASP217 4.1 59.4 1.0 CG B:ASP217 4.1 62.0 1.0 OD1 B:ASP216 4.2 46.8 1.0 NE2 B:GLN246 4.3 50.9 1.0 CB B:ASP189 4.5 59.5 1.0 C B:ASP216 4.6 50.1 1.0 NH2 B:ARG61 4.6 46.5 1.0 CA B:ASP189 4.6 58.6 1.0 O B:ASP216 4.7 51.4 1.0 N B:ASP217 4.7 52.4 1.0 C B:ASP189 4.8 61.1 1.0 O B:ASP189 4.8 63.3 1.0 CB B:ASP191 4.8 68.2 1.0 CA B:ASP216 4.9 48.0 1.0 CA B:ASP217 5.0 55.9 1.0

S.M.Bernard, D.L.Akey, A.Tripathi, S.R.Park, J.R.Konwerski, Y.Anzai, S.Li, F.Kato, D.H.Sherman, J.L.Smith. Structural Basis of Substrate Specificity and Regiochemistry in the Mycf/Tylf Family of Sugar O-Methyltransferases. Acs Chem.Biol. 2015.
ISSN: ESSN 1554-8937
PubMed: 25692963
DOI: 10.1021/CB5009348