Magnesium in PDB 1bs1: 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: 1bs1 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 (°)	72.900, 48.200, 60.900, 90.00, 107.00, 90.00
R / Rfree (%)	17.2 / 20.6

The structure of Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Aluminium	(Al)	1 atom

The binding sites of Magnesium atom in the Dethiobiotin Synthetase Complexed with Dethiobiotin, Adp , Inorganic Phosphate and Magnesium (pdb code 1bs1). 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: 1bs1:
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:20.2 occ:1.00 O2B A:ADP802 2.0 9.8 1.0 F1 A:DAA850 2.1 18.1 1.0 OG1 A:THR16 2.1 8.4 1.0 OE2 A:GLU115 2.2 12.1 1.0 OD2 A:ASP54 2.2 9.4 1.0 O A:HOH444 2.4 23.8 1.0 CG A:ASP54 3.0 9.9 1.0 PB A:ADP802 3.3 11.0 1.0 CD A:GLU115 3.3 11.7 1.0 OD1 A:ASP54 3.3 7.9 1.0 CB A:THR16 3.4 8.7 1.0 O3B A:ADP802 3.5 10.7 1.0 AL A:DAA850 3.6 14.2 1.0 N A:THR16 3.7 8.2 1.0 MG A:MG902 3.7 16.0 1.0 OE1 A:GLU115 3.8 13.5 1.0 NZ A:LYS37 3.8 7.5 1.0 CA A:THR16 4.0 8.0 1.0 F2 A:DAA850 4.1 19.4 1.0 CB A:ASP54 4.1 8.8 1.0 O1A A:ADP802 4.1 12.6 1.0 O3A A:ADP802 4.3 12.1 1.0 CE A:LYS15 4.3 13.3 1.0 O1B A:ADP802 4.3 10.3 1.0 CB A:LYS15 4.4 11.6 1.0 CG2 A:THR16 4.5 9.2 1.0 F3 A:DAA850 4.5 17.3 1.0 PA A:ADP802 4.6 12.9 1.0 CG A:GLU115 4.6 10.4 1.0 NZ A:LYS15 4.6 15.6 1.0 O11 A:DAA850 4.7 15.7 1.0 C A:LYS15 4.7 9.6 1.0 O A:HOH717 4.7 13.6 1.0 O2A A:ADP802 4.8 12.6 1.0 CE A:LYS37 5.0 8.0 1.0 CA A:LYS15 5.0 10.6 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:16.0 occ:1.00 O3B A:ADP802 2.2 10.7 1.0 O A:HOH444 2.2 23.8 1.0 F2 A:DAA850 2.3 19.4 1.0 O A:HOH754 2.4 17.4 1.0 O A:HOH836 3.0 26.8 1.0 OE1 A:GLU12 3.2 24.8 1.0 F1 A:DAA850 3.3 18.1 1.0 AL A:DAA850 3.4 14.2 1.0 PB A:ADP802 3.4 11.0 1.0 O2B A:ADP802 3.7 9.8 1.0 MG A:MG901 3.7 20.2 1.0 O A:HOH832 3.7 35.1 1.0 O A:HOH833 3.8 24.9 1.0 O1A A:ADP802 3.9 12.6 1.0 N2 A:DAA850 3.9 19.0 1.0 F3 A:DAA850 3.9 17.3 1.0 O3A A:ADP802 4.1 12.1 1.0 OG1 A:THR11 4.1 11.7 1.0 O A:HOH717 4.2 13.6 1.0 OD2 A:ASP54 4.2 9.4 1.0 CD A:GLU12 4.3 21.8 1.0 OD1 A:ASP54 4.3 7.9 1.0 N A:GLU12 4.4 10.7 1.0 PA A:ADP802 4.7 12.9 1.0 O1B A:ADP802 4.7 10.3 1.0 CG A:ASP54 4.7 9.9 1.0 O11 A:DAA850 4.7 15.7 1.0 CA A:GLU12 4.8 12.8 1.0 OE2 A:GLU12 4.8 25.6 1.0 CH A:DAA850 4.9 17.2 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