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

Enzymatic activity of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gtp

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

Protein crystallography data

The structure of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gtp, PDB code: 3qxj was solved by M.M.Klimecka, P.J.Porebski, 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 / 1.38
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.151, 37.504, 69.095, 90.00, 101.23, 90.00
R / Rfree (%) 15.9 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gtp (pdb code 3qxj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gtp, PDB code: 3qxj:

Magnesium binding site 1 out of 1 in 3qxj

Go back to Magnesium Binding Sites List in 3qxj
Magnesium binding site 1 out of 1 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg224

b:13.6
occ:1.00
 O3G A:GTP221 2.0 13.9 0.8
OD2 A:ASP50 2.1 13.6 1.0
OG1 A:THR14 2.1 13.2 1.0
O1B A:GTP221 2.1 12.2 0.8
OE2 A:GLU116 2.1 13.0 1.0
O A:HOH374 2.2 12.3 1.0
CG A:ASP50 2.9 14.6 1.0
PG A:GTP221 3.1 15.1 0.8
CD A:GLU116 3.1 12.3 1.0
PB A:GTP221 3.3 12.7 0.8
CB A:THR14 3.3 12.7 1.0
OD1 A:ASP50 3.3 16.9 1.0
O3B A:GTP221 3.3 13.2 0.8
OE1 A:GLU116 3.4 15.8 1.0
N A:THR14 3.8 12.9 1.0
O A:HOH520 3.8 29.1 1.0
NZ A:LYS35 3.8 13.0 1.0
O2G A:GTP221 3.9 14.2 0.8
CA A:THR14 4.1 12.2 1.0
CB A:ASP50 4.1 13.6 1.0
O1G A:GTP221 4.2 16.9 0.8
O2A A:GTP221 4.2 18.0 0.8
O3A A:GTP221 4.3 14.0 0.8
O2B A:GTP221 4.3 12.5 0.8
CG2 A:THR14 4.3 13.2 1.0
CE A:LYS13 4.4 13.5 1.0
CG A:GLU116 4.5 11.5 1.0
CB A:LYS13 4.5 12.3 1.0
O2 A:EDO232 4.5 24.3 1.0
PA A:GTP221 4.7 16.0 0.8
CE A:LYS35 4.7 12.6 1.0
NZ A:LYS13 4.8 14.7 1.0
C A:LYS13 4.8 13.1 1.0
O A:HOH468 4.9 33.8 1.0
O1A A:GTP221 5.0 15.4 0.8

Reference:

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
Page generated: Mon Aug 11 02:32:12 2025

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