Magnesium in PDB 1dak: Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride

All present enzymatic activity of Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride:
6.3.3.3;

The structure of Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride, PDB code: 1dak was solved by H.Kaeck, K.J.Gibson, Y.Lindqvist, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.680, 48.190, 61.070, 90.00, 106.58, 90.00
R / Rfree (%)	18.4 / 21

The binding sites of Magnesium atom in the Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride (pdb code 1dak). 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 From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride, PDB code: 1dak:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:11.8 occ:1.00 O3B A:ADP802 2.0 12.1 1.0 OD2 A:ASP54 2.1 11.8 1.0 OE2 A:GLU115 2.2 10.8 1.0 O2B A:DPU801 2.2 16.4 1.0 OG1 A:THR16 2.3 7.8 1.0 O A:HOH444 2.3 14.0 1.0 CG A:ASP54 3.0 11.8 1.0 CD A:GLU115 3.3 10.4 1.0 PB A:ADP802 3.3 12.9 1.0 O2B A:ADP802 3.4 13.0 1.0 OD1 A:ASP54 3.4 11.7 1.0 PB A:DPU801 3.4 18.5 1.0 CB A:THR16 3.5 9.2 1.0 OE1 A:GLU115 3.6 12.2 1.0 O3B A:DPU801 3.6 15.7 1.0 MG A:MG902 3.6 12.0 1.0 N A:THR16 3.8 8.9 1.0 NZ A:LYS37 3.9 10.9 1.0 O1A A:ADP802 4.0 14.6 1.0 CA A:THR16 4.2 7.9 1.0 CB A:ASP54 4.2 10.7 1.0 O3A A:ADP802 4.3 13.3 1.0 O1B A:ADP802 4.3 12.0 1.0 CE A:LYS15 4.3 10.8 1.0 CB A:LYS15 4.3 10.3 1.0 O1B A:DPU801 4.4 16.3 1.0 O2A A:DPU801 4.4 15.4 1.0 PA A:ADP802 4.6 14.6 1.0 CG A:GLU115 4.6 10.0 1.0 NZ A:LYS15 4.6 11.3 1.0 CG2 A:THR16 4.6 10.6 1.0 C A:LYS15 4.7 9.7 1.0 O A:HOH717 4.7 25.1 1.0 O2A A:ADP802 4.9 13.1 1.0 O A:HOH754 4.9 17.4 1.0 CA A:LYS15 4.9 10.6 1.0

Magnesium binding site 2 out of 2 in the Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dethiobiotin Synthetase From Escherichia Coli, Complex Reaction Intermediate Adp and Mixed Anhydride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:12.0 occ:1.00 O A:HOH444 2.1 14.0 1.0 O2B A:ADP802 2.1 13.0 1.0 O A:HOH754 2.1 17.4 1.0 O3B A:DPU801 2.1 15.7 1.0 O A:HOH429 2.2 15.2 1.0 O A:HOH559 2.3 22.9 1.0 PB A:DPU801 3.3 18.5 1.0 PB A:ADP802 3.4 12.9 1.0 O2B A:DPU801 3.6 16.4 1.0 N2 A:DPU801 3.6 14.0 1.0 MG A:MG901 3.6 11.8 1.0 O3B A:ADP802 3.7 12.1 1.0 O1A A:ADP802 3.7 14.6 1.0 OE1 A:GLU12 3.9 23.3 1.0 O2A A:DPU801 4.0 15.4 1.0 OG1 A:THR11 4.0 11.8 1.0 O3A A:ADP802 4.1 13.3 1.0 OD2 A:ASP54 4.3 11.8 1.0 OD1 A:ASP54 4.3 11.7 1.0 N A:GLU12 4.3 11.4 1.0 O A:HOH717 4.4 25.1 1.0 PA A:ADP802 4.6 14.6 1.0 CA A:GLU12 4.6 12.7 1.0 O1B A:ADP802 4.6 12.0 1.0 O1B A:DPU801 4.6 16.3 1.0 O A:HOH755 4.7 23.8 1.0 CG A:ASP54 4.7 11.8 1.0 CD A:GLU12 4.7 21.5 1.0 CH A:DPU801 4.9 13.7 1.0

H.Kack, K.J.Gibson, Y.Lindqvist, G.Schneider. Snapshot of A Phosphorylated Substrate Intermediate By Kinetic Crystallography. Proc.Natl.Acad.Sci.Usa V. 95 5495 1998.
ISSN: ISSN 0027-8424
PubMed: 9576910
DOI: 10.1073/PNAS.95.10.5495