Magnesium in PDB 3sso: Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2

The structure of Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2, PDB code: 3sso 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)	49.16 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	144.220, 250.846, 158.315, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 17.7

The binding sites of Magnesium atom in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2 (pdb code 3sso). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2, PDB code: 3sso:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:26.6 occ:1.00 O A:HOH2240 2.2 44.8 1.0 OD1 A:ASP275 2.3 20.2 1.0 O A:HOH2050 2.4 39.0 1.0 OE1 A:GLU303 2.5 25.5 1.0 O A:HOH2360 2.6 56.0 1.0 OD2 A:ASP304 2.6 30.8 1.0 OD2 A:ASP275 2.8 17.4 1.0 CG A:ASP275 2.8 18.7 1.0 O A:HOH2051 2.9 32.2 1.0 CG A:ASP304 3.7 27.1 1.0 CD A:GLU303 3.7 24.8 1.0 OD1 A:ASP304 4.0 30.8 1.0 NE2 A:HIS278 4.3 16.6 1.0 CE1 A:HIS278 4.3 18.4 1.0 CB A:ASP275 4.3 16.3 1.0 CG A:GLU303 4.4 27.0 1.0 NZ A:LYS175 4.4 28.0 1.0 O A:HOH2239 4.6 42.7 1.0 O A:HOH2238 4.6 41.3 1.0 OE2 A:GLU303 4.7 25.7 1.0 CB A:GLU303 4.7 20.7 1.0 OXT A:SAH601 4.9 22.0 1.0 CE2 A:PHE182 4.9 16.9 1.0 CB A:ASP304 4.9 22.3 1.0 CB A:SAH601 4.9 17.9 1.0 O A:ASP275 5.0 16.3 1.0

Magnesium binding site 2 out of 6 in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:34.1 occ:1.00 O B:HOH2806 2.0 51.6 1.0 OD1 B:ASP275 2.3 26.6 1.0 OD2 B:ASP304 2.5 33.3 1.0 OE1 B:GLU303 2.5 26.2 1.0 O B:HOH1978 2.6 37.8 1.0 OD2 B:ASP275 2.8 22.3 1.0 CG B:ASP275 2.8 24.5 1.0 O B:HOH1276 3.0 37.8 1.0 CG B:ASP304 3.5 30.5 1.0 CD B:GLU303 3.7 25.4 1.0 OD1 B:ASP304 4.0 30.4 1.0 CE1 B:HIS278 4.2 22.1 1.0 CB B:ASP275 4.3 21.3 1.0 CG B:GLU303 4.3 26.1 1.0 NE2 B:HIS278 4.3 22.1 1.0 O B:HOH1600 4.5 47.4 1.0 NZ B:LYS175 4.6 26.7 1.0 CB B:GLU303 4.6 24.6 1.0 OE2 B:GLU303 4.7 24.1 1.0 CE2 B:PHE182 4.7 20.6 1.0 CB B:ASP304 4.7 24.6 1.0 NE2 B:HIS180 4.9 28.0 1.0 O B:HOH1874 4.9 51.3 1.0 CA B:ASP275 5.0 19.4 1.0 O B:ASP275 5.0 20.2 1.0

Magnesium binding site 3 out of 6 in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:26.5 occ:1.00 OD1 C:ASP275 2.2 21.6 1.0 O C:HOH2065 2.3 33.4 1.0 O C:HOH2064 2.3 31.7 1.0 OE1 C:GLU303 2.5 24.9 1.0 OD2 C:ASP304 2.6 30.4 1.0 OD2 C:ASP275 2.7 18.5 1.0 CG C:ASP275 2.8 20.3 1.0 O C:HOH2063 2.9 31.5 1.0 O C:HOH2275 3.0 52.8 1.0 CG C:ASP304 3.6 27.6 1.0 CD C:GLU303 3.7 24.6 1.0 OD1 C:ASP304 4.0 27.8 1.0 CB C:ASP275 4.3 17.3 1.0 CE1 C:HIS278 4.3 17.4 1.0 NE2 C:HIS278 4.4 17.5 1.0 CG C:GLU303 4.4 26.7 1.0 NZ C:LYS175 4.4 25.1 1.0 O C:HOH855 4.6 42.7 1.0 OE2 C:GLU303 4.6 24.0 1.0 CB C:GLU303 4.7 21.3 1.0 O C:HOH2066 4.7 39.3 1.0 CE2 C:PHE182 4.8 17.1 1.0 OXT C:SAH601 4.8 21.1 1.0 CB C:ASP304 4.9 24.5 1.0 CA C:ASP275 5.0 15.9 1.0 CB C:SAH601 5.0 18.9 1.0

Magnesium binding site 4 out of 6 in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:34.8 occ:1.00 O D:HOH2807 2.0 52.3 1.0 OD1 D:ASP275 2.2 26.6 1.0 OD2 D:ASP304 2.5 36.0 1.0 O D:HOH1998 2.5 35.9 1.0 OE1 D:GLU303 2.7 24.6 1.0 OD2 D:ASP275 2.8 25.6 1.0 CG D:ASP275 2.8 23.7 1.0 O D:HOH1356 2.8 36.2 1.0 CG D:ASP304 3.5 33.2 1.0 CD D:GLU303 3.9 25.9 1.0 OD1 D:ASP304 4.0 32.5 1.0 CE1 D:HIS278 4.2 23.2 1.0 CB D:ASP275 4.3 21.1 1.0 NE2 D:HIS278 4.3 21.9 1.0 CB D:GLU303 4.5 24.1 1.0 NZ D:LYS175 4.6 24.9 1.0 O D:HOH2109 4.6 50.5 1.0 CE2 D:PHE182 4.7 21.5 1.0 CG D:GLU303 4.7 26.3 1.0 CB D:ASP304 4.8 28.1 1.0 OE2 D:GLU303 4.8 23.8 1.0 NE2 D:HIS180 4.9 27.3 1.0 CA D:ASP275 5.0 17.3 1.0

Magnesium binding site 5 out of 6 in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:34.9 occ:1.00 O E:HOH2397 2.0 44.9 1.0 OD1 E:ASP275 2.2 28.2 1.0 OE1 E:GLU303 2.4 25.5 1.0 OD2 E:ASP304 2.4 33.8 1.0 O E:HOH1977 2.4 38.8 1.0 OD2 E:ASP275 2.8 23.9 1.0 CG E:ASP275 2.8 25.8 1.0 O E:HOH1354 3.0 41.7 1.0 CG E:ASP304 3.5 31.4 1.0 CD E:GLU303 3.6 25.3 1.0 OD1 E:ASP304 3.9 32.4 1.0 CG E:GLU303 4.2 26.3 1.0 CE1 E:HIS278 4.2 22.6 1.0 CB E:ASP275 4.3 22.5 1.0 NE2 E:HIS278 4.4 22.5 1.0 O E:HOH447 4.5 46.4 1.0 CB E:GLU303 4.5 24.8 1.0 OE2 E:GLU303 4.6 23.2 1.0 NZ E:LYS175 4.6 25.4 1.0 CE2 E:PHE182 4.6 20.3 1.0 CB E:ASP304 4.7 26.6 1.0 OXT E:SAH601 4.9 29.7 1.0 NE2 E:HIS180 4.9 30.2 1.0 CA E:ASP275 5.0 19.5 1.0

Magnesium binding site 6 out of 6 in the Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Myce Methyltransferase From the Mycinamycin Biosynthetic Pathway in Complex with Mg and Sah, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:27.0 occ:1.00 O F:HOH2061 2.2 36.5 1.0 OD1 F:ASP275 2.3 19.7 1.0 O F:HOH2060 2.3 32.3 1.0 OE1 F:GLU303 2.4 26.8 1.0 OD2 F:ASP304 2.6 30.2 1.0 OD2 F:ASP275 2.8 18.8 1.0 CG F:ASP275 2.8 19.9 1.0 O F:HOH2059 3.0 38.7 1.0 CG F:ASP304 3.6 27.8 1.0 CD F:GLU303 3.6 26.4 1.0 OD1 F:ASP304 4.0 29.1 1.0 O F:HOH2579 4.2 58.2 1.0 CB F:ASP275 4.3 17.0 1.0 CG F:GLU303 4.3 27.0 1.0 CE1 F:HIS278 4.3 16.9 1.0 NE2 F:HIS278 4.4 15.8 1.0 NZ F:LYS175 4.4 27.0 1.0 OE2 F:GLU303 4.6 26.2 1.0 CB F:GLU303 4.6 20.1 1.0 O F:HOH2062 4.7 41.4 1.0 CE2 F:PHE182 4.7 17.9 1.0 O F:HOH460 4.7 47.1 1.0 OXT F:SAH601 4.8 22.4 1.0 CB F:ASP304 4.9 23.6 1.0

D.L.Akey, S.Li, J.R.Konwerski, L.A.Confer, S.M.Bernard, Y.Anzai, F.Kato, D.H.Sherman, J.L.Smith. A New Structural Form in the Sam/Metal-Dependent O‑Methyltransferase Family: Myce From the Mycinamicin Biosynthetic Pathway. J.Mol.Biol. V. 413 438 2011.
ISSN: ISSN 0022-2836
PubMed: 21884704
DOI: 10.1016/J.JMB.2011.08.040