Magnesium in PDB 3qy0: Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp

All present enzymatic activity of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp:
6.3.3.3;

The structure of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp, PDB code: 3qy0 was solved by P.J.Porebski, M.M.Klimecka, M.Chruszcz, K.Murzyn, A.Joachimiak, W.Minor, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.718, 37.342, 69.125, 90.00, 101.46, 90.00
R / Rfree (%)	13.9 / 17.1

The binding sites of Magnesium atom in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp (pdb code 3qy0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp, PDB code: 3qy0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg223 b:23.4 occ:1.00 O1B A:GDP221 2.0 17.3 1.0 O3 A:PO4222 2.1 28.4 0.8 O A:HOH420 2.1 24.4 1.0 O A:HOH430 2.1 24.6 1.0 O A:HOH429 2.2 25.4 1.0 O A:HOH270 2.5 9.0 1.0 O1 A:PO4222 2.7 17.3 0.8 P A:PO4222 3.0 22.9 0.8 PB A:GDP221 3.4 13.4 1.0 OG1 A:THR9 3.5 30.1 1.0 MG A:MG224 3.6 12.6 1.0 O3B A:GDP221 3.7 13.9 1.0 O2 A:PO4222 3.8 26.2 0.8 OD1 A:ASN10 3.9 31.2 1.0 N A:ASN10 4.0 18.4 1.0 O1A A:GDP221 4.0 17.5 1.0 O4 A:PO4222 4.1 19.4 0.8 O3A A:GDP221 4.1 15.3 1.0 O A:HOH396 4.2 22.1 1.0 OD2 A:ASP50 4.4 11.3 1.0 O2B A:GDP221 4.4 12.2 1.0 CA A:ASN10 4.6 19.6 1.0 OD1 A:ASP50 4.6 15.3 1.0 PA A:GDP221 4.7 19.8 1.0 CB A:THR9 4.8 23.9 1.0 CG A:ASN10 4.8 25.2 1.0 NZ A:LYS13 4.9 14.8 1.0 C A:THR9 4.9 21.3 1.0 CG A:ASP50 5.0 10.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg224 b:12.6 occ:1.00 O3B A:GDP221 2.0 13.9 1.0 O1 A:PO4222 2.0 17.3 0.8 OE2 A:GLU116 2.1 12.3 1.0 OD2 A:ASP50 2.1 11.3 1.0 OG1 A:THR14 2.1 13.7 1.0 O A:HOH270 2.1 9.0 1.0 CG A:ASP50 2.9 10.2 1.0 CD A:GLU116 3.1 10.4 1.0 PB A:GDP221 3.3 13.4 1.0 CB A:THR14 3.3 12.2 1.0 OD1 A:ASP50 3.3 15.3 1.0 O1B A:GDP221 3.4 17.3 1.0 OE1 A:GLU116 3.4 13.3 1.0 P A:PO4222 3.5 22.9 0.8 MG A:MG223 3.6 23.4 1.0 NZ A:LYS35 3.8 10.8 1.0 N A:THR14 3.8 11.1 1.0 O1A A:GDP221 3.9 17.5 1.0 O3 A:PO4222 4.0 28.4 0.8 CA A:THR14 4.1 11.6 1.0 CB A:ASP50 4.1 10.4 1.0 O4 A:PO4222 4.2 19.4 0.8 O3A A:GDP221 4.3 15.3 1.0 O2B A:GDP221 4.3 12.2 1.0 CE A:LYS13 4.4 14.2 1.0 CB A:LYS13 4.4 9.6 1.0 CG A:GLU116 4.4 9.4 1.0 CG2 A:THR14 4.4 11.8 1.0 NZ A:LYS13 4.5 14.8 1.0 PA A:GDP221 4.5 19.8 1.0 O2 A:PO4222 4.6 26.2 0.8 O A:HOH429 4.6 25.4 1.0 CE A:LYS35 4.7 10.0 1.0 C A:LYS13 4.8 11.5 1.0 O A:HOH420 4.8 24.4 1.0 O A:HOH396 4.8 22.1 1.0

P.J.Porebski, M.Klimecka, M.Chruszcz, R.A.Nicholls, K.Murzyn, M.E.Cuff, X.Xu, M.Cymborowski, G.N.Murshudov, A.Savchenko, A.Edwards, W.Minor. Structural Characterization of Helicobacter Pylori Dethiobiotin Synthetase Reveals Differences Between Family Members. Febs J. V. 279 1093 2012.
ISSN: ISSN 1742-464X
PubMed: 22284390
DOI: 10.1111/J.1742-4658.2012.08506.X