Atomistry » Magnesium » PDB 3qpp-3r10 » 3qxx
Atomistry »
  Magnesium »
    PDB 3qpp-3r10 »
      3qxx »

Magnesium in PDB 3qxx: Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp and 8-Aminocaprylic Acid

Enzymatic activity of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp and 8-Aminocaprylic Acid

All present enzymatic activity of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp and 8-Aminocaprylic Acid:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp and 8-Aminocaprylic Acid, PDB code: 3qxx 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 / 1.36
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.883, 37.845, 68.839, 90.00, 101.30, 90.00
R / Rfree (%) 13 / 16.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp and 8-Aminocaprylic Acid (pdb code 3qxx). 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 and 8-Aminocaprylic Acid, PDB code: 3qxx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3qxx

Go back to Magnesium Binding Sites List in 3qxx
Magnesium binding site 1 out of 2 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp and 8-Aminocaprylic Acid


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 and 8-Aminocaprylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg223

b:13.4
occ:1.00
O3 A:PO4225 2.0 16.0 1.0
O1B A:GDP222 2.0 11.4 1.0
O A:HOH290 2.1 18.6 1.0
O A:HOH289 2.2 16.1 1.0
O A:HOH269 2.2 18.6 1.0
O A:HOH517 2.2 12.0 1.0
P A:PO4225 3.1 12.8 1.0
O1 A:PO4225 3.1 14.6 1.0
PB A:GDP222 3.3 10.9 1.0
MG A:MG224 3.6 10.5 1.0
O3B A:GDP222 3.8 10.2 1.0
O1A A:GDP222 3.8 13.3 1.0
OG1 A:THR9 3.8 15.6 1.0
O2 A:PO4225 3.9 12.5 1.0
NAA A:8AC221 3.9 19.4 1.0
O A:HOH493 3.9 17.7 1.0
O3A A:GDP222 4.1 11.4 1.0
OD1 A:ASN10 4.2 25.7 0.5
N A:ASN10 4.2 11.4 1.0
O4 A:PO4225 4.3 14.2 1.0
OD1 A:ASN10 4.3 25.7 0.5
OD2 A:ASP50 4.4 10.2 1.0
O A:HOH298 4.4 30.0 1.0
OD1 A:ASP50 4.4 12.5 1.0
O A:HOH307 4.5 46.0 1.0
O2B A:GDP222 4.5 10.9 1.0
PA A:GDP222 4.6 12.8 1.0
CA A:ASN10 4.6 12.4 0.5
CA A:ASN10 4.7 12.4 0.5
CG A:ASN10 4.8 18.5 0.5
CG A:ASP50 4.9 10.6 1.0

Magnesium binding site 2 out of 2 in 3qxx

Go back to Magnesium Binding Sites List in 3qxx
Magnesium binding site 2 out of 2 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Gdp and 8-Aminocaprylic Acid


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 and 8-Aminocaprylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg224

b:10.5
occ:1.00
O3B A:GDP222 2.0 10.2 1.0
OE2 A:GLU116 2.1 9.8 1.0
O1 A:PO4225 2.1 14.6 1.0
OD2 A:ASP50 2.1 10.2 1.0
O A:HOH517 2.2 12.0 1.0
OG1 A:THR14 2.2 10.2 1.0
CG A:ASP50 3.0 10.6 1.0
CD A:GLU116 3.1 9.8 1.0
PB A:GDP222 3.2 10.9 1.0
OD1 A:ASP50 3.3 12.5 1.0
CB A:THR14 3.4 10.5 1.0
P A:PO4225 3.4 12.8 1.0
O1B A:GDP222 3.4 11.4 1.0
OE1 A:GLU116 3.5 13.1 1.0
MG A:MG223 3.6 13.4 1.0
NZ A:LYS35 3.7 11.5 1.0
N A:THR14 3.8 9.6 1.0
O3 A:PO4225 3.8 16.0 1.0
O1A A:GDP222 4.1 13.3 1.0
CA A:THR14 4.1 9.2 1.0
O4 A:PO4225 4.2 14.2 1.0
CB A:ASP50 4.2 10.8 1.0
O2B A:GDP222 4.2 10.9 1.0
CE A:LYS13 4.3 12.5 1.0
CB A:LYS13 4.3 9.4 1.0
O3A A:GDP222 4.3 11.4 1.0
CG A:GLU116 4.4 10.2 1.0
O A:HOH493 4.4 17.7 1.0
NZ A:LYS13 4.5 14.5 1.0
O2 A:PO4225 4.5 12.5 1.0
CG2 A:THR14 4.5 11.1 1.0
O A:HOH289 4.6 16.1 1.0
PA A:GDP222 4.6 12.8 1.0
CE A:LYS35 4.7 10.0 1.0
C A:LYS13 4.8 9.4 1.0
O A:HOH269 4.9 18.6 1.0
CA A:LYS13 5.0 9.4 1.0

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: Thu Aug 15 10:13:34 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy