Magnesium in PDB 5bp2: Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1

The structure of Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1, PDB code: 5bp2 was solved by D.A.Herbst, P.R.Jakob, F.Zaehringer, T.Maier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.60 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.650, 162.400, 66.620, 90.00, 91.38, 90.00
R / Rfree (%)	18.3 / 20.3

The structure of Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1 (pdb code 5bp2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1, PDB code: 5bp2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:88.0 occ:1.00 OD1 A:ASP978 2.6 73.2 1.0 OE2 A:GLU926 2.7 79.7 0.5 OG1 A:THR925 2.9 62.7 1.0 HG1 A:THR925 3.1 63.5 1.0 HA A:ASP978 3.2 60.8 1.0 HB A:THR925 3.4 62.5 1.0 HA A:GLU926 3.4 59.8 0.5 HA A:GLU926 3.5 60.1 0.5 O A:HOH1416 3.5 74.4 1.0 N A:GLU926 3.6 58.5 0.5 N A:GLU926 3.6 58.9 0.5 HB2 A:GLU926 3.6 62.2 0.5 CB A:THR925 3.6 62.1 1.0 HB2 A:GLU926 3.6 62.6 0.5 CG A:ASP978 3.6 72.7 1.0 C A:THR925 3.7 60.0 1.0 H A:GLU926 3.8 58.9 0.5 H A:GLU926 3.8 59.3 0.5 CD A:GLU926 3.8 94.4 0.5 CA A:GLU926 3.9 59.6 0.5 CA A:GLU926 3.9 59.1 0.5 O A:THR925 4.0 59.9 1.0 CA A:ASP978 4.1 60.8 1.0 HB3 A:ASP978 4.2 64.7 1.0 CB A:ASP978 4.2 64.1 1.0 CA A:THR925 4.2 54.2 1.0 CB A:GLU926 4.2 62.5 0.5 CB A:GLU926 4.3 61.6 0.5 O A:HOH1351 4.4 79.9 1.0 OD2 A:ASP978 4.6 83.8 1.0 CG A:GLU926 4.6 75.0 0.5 H A:THR925 4.7 55.8 1.0 OE1 A:GLU926 4.7 91.3 0.5 HG A:SER932 4.8 65.4 1.0 O A:HOH1348 4.8 71.8 1.0 N A:ASP978 4.9 61.2 1.0 N A:THR925 4.9 55.0 1.0 HG3 A:GLU926 4.9 71.2 0.5 CG2 A:THR925 5.0 59.9 1.0

Magnesium binding site 2 out of 2 in the Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dehydratase Domain (Dh) of A Mycocerosic Acid Synthase-Like (Mas-Like) Pks, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1201 b:63.9 occ:1.00 OD1 D:ASP972 2.0 51.8 1.0 O D:HOH1331 2.0 55.0 1.0 O D:HOH1372 2.1 67.7 1.0 O D:HOH1454 2.1 59.7 1.0 O D:HOH1350 2.3 72.0 1.0 CG D:ASP972 3.1 55.8 1.0 HH22 D:ARG1009 3.3 50.8 1.0 OD2 D:ASP972 3.5 55.2 1.0 O D:MET973 3.9 49.7 1.0 NH2 D:ARG1009 4.1 49.7 1.0 HA D:ASP972 4.1 44.8 1.0 H D:MET973 4.2 49.4 1.0 HH21 D:ARG1009 4.3 49.5 1.0 CB D:ASP972 4.4 48.4 1.0 N D:MET973 4.5 47.5 1.0 HG21 D:THR1007 4.5 53.2 1.0 C D:ASP972 4.5 49.1 1.0 O D:HOH1366 4.5 61.1 1.0 CA D:ASP972 4.6 45.9 1.0 HH12 D:ARG1009 4.6 52.2 1.0 C D:MET973 4.9 49.5 1.0 HB3 D:ASP972 4.9 48.1 1.0 HB2 D:MET973 5.0 55.0 1.0

D.A.Herbst, R.P.Jakob, F.Zahringer, T.Maier. Mycocerosic Acid Synthase Exemplifies the Architecture of Reducing Polyketide Synthases. Nature V. 531 533 2016.
ISSN: ESSN 1476-4687
PubMed: 26976449
DOI: 10.1038/NATURE16993