Magnesium in PDB 1dam: Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium

All present enzymatic activity of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium:
6.3.3.3;

The structure of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium, PDB code: 1dam was solved by H.Kaeck, J.Sandmark, K.J.Gibson, G.Schneider, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.700, 48.900, 61.100, 90.00, 106.70, 90.00
R / Rfree (%)	18 / 23.3

The binding sites of Magnesium atom in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium (pdb code 1dam). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium, PDB code: 1dam:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:18.7 occ:1.00 O2B A:ADP801 2.0 13.6 1.0 OE2 A:GLU115 2.0 14.7 1.0 O2 A:PO4802 2.0 15.7 1.0 OD2 A:ASP54 2.1 14.3 1.0 OG1 A:THR16 2.2 11.4 1.0 O A:HOH444 2.8 22.1 1.0 CG A:ASP54 3.0 12.7 1.0 CD A:GLU115 3.1 16.3 1.0 PB A:ADP801 3.3 14.6 1.0 CB A:THR16 3.4 12.7 1.0 O3B A:ADP801 3.5 14.7 1.0 P A:PO4802 3.5 18.4 1.0 OE1 A:GLU115 3.5 17.0 1.0 OD1 A:ASP54 3.5 12.7 1.0 N A:THR16 3.7 12.2 1.0 MG A:MG902 3.7 15.6 1.0 NZ A:LYS37 3.8 13.8 1.0 O3 A:PO4802 3.8 17.3 1.0 CA A:THR16 4.0 12.2 1.0 CB A:LYS15 4.0 10.5 1.0 CB A:ASP54 4.1 12.7 1.0 O1B A:ADP801 4.2 14.0 1.0 O1A A:ADP801 4.2 13.7 1.0 CE A:LYS15 4.3 12.0 1.0 O1 A:PO4802 4.3 16.9 1.0 O3A A:ADP801 4.4 14.5 1.0 CG A:GLU115 4.4 14.9 1.0 NZ A:LYS15 4.5 11.7 1.0 C A:LYS15 4.5 12.3 1.0 O4 A:PO4802 4.5 17.1 1.0 CG2 A:THR16 4.6 12.7 1.0 PA A:ADP801 4.6 14.6 1.0 CA A:LYS15 4.8 12.2 1.0 O2A A:ADP801 4.8 12.7 1.0 O A:HOH749 4.9 19.4 1.0 CE A:LYS37 5.0 11.6 1.0 N A:LYS15 5.0 12.4 1.0

Magnesium binding site 2 out of 2 in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp, Inorganic Phosphate and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:15.6 occ:1.00 O3B A:ADP801 1.9 14.7 1.0 O A:HOH749 2.1 19.4 1.0 O A:HOH444 2.1 22.1 1.0 O A:HOH448 2.2 14.9 1.0 O3 A:PO4802 2.2 17.3 1.0 O A:HOH750 2.4 19.3 1.0 PB A:ADP801 3.2 14.6 1.0 P A:PO4802 3.4 18.4 1.0 O2 A:PO4802 3.4 15.7 1.0 O2B A:ADP801 3.5 13.6 1.0 O1A A:ADP801 3.6 13.7 1.0 MG A:MG901 3.7 18.7 1.0 O3A A:ADP801 3.9 14.5 1.0 O A:DTB803 3.9 24.8 1.0 O4 A:PO4802 4.0 17.1 1.0 OG1 A:THR11 4.0 18.3 1.0 OD2 A:ASP54 4.1 14.3 1.0 OD1 A:ASP54 4.2 12.7 1.0 N A:GLU12 4.3 18.9 1.0 O A:HOH717 4.4 22.1 1.0 O1B A:ADP801 4.4 14.0 1.0 PA A:ADP801 4.4 14.6 1.0 CA A:GLU12 4.6 19.5 1.0 O1 A:PO4802 4.6 16.9 1.0 CG A:ASP54 4.6 12.7 1.0 O A:HOH718 4.7 47.7 1.0 CN A:DTB803 4.8 24.6 1.0 N2 A:DTB803 4.9 23.5 1.0

H.Kack, J.Sandmark, K.J.Gibson, G.Schneider, Y.Lindqvist. Crystal Structure of Two Quaternary Complexes of Dethiobiotin Synthetase, Enzyme-Mgadp-ALF3-Diaminopelargonic Acid and Enzyme-Mgadp-Dethiobiotin-Phosphate; Implications For Catalysis. Protein Sci. V. 7 2560 1998.
ISSN: ISSN 0961-8368
PubMed: 9865950