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

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

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

All present enzymatic activity of Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Adp 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 Adp and 8-Aminocaprylic Acid, PDB code: 3qxh was solved by P.J.Porebski, M.M.Klimecka, M.Chruszcz, K.Murzyn, C.Minor, 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 (°) 81.526, 37.967, 68.795, 90.00, 101.15, 90.00
R / Rfree (%) 11.7 / 14.2

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 3qxh

Go back to Magnesium Binding Sites List in 3qxh
Magnesium binding site 1 out of 2 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Adp 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 Adp and 8-Aminocaprylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg223

b:6.2
occ:1.00
O1 A:PO4225 2.0 9.1 1.0
O1B A:ADP222 2.0 6.2 1.0
OE2 A:GLU116 2.1 5.9 1.0
OD2 A:ASP50 2.1 6.5 1.0
OG1 A:THR14 2.2 6.2 1.0
O A:HOH337 2.2 7.9 1.0
CG A:ASP50 3.0 6.8 1.0
CD A:GLU116 3.1 5.8 1.0
PB A:ADP222 3.2 6.2 1.0
OD1 A:ASP50 3.4 7.7 1.0
CB A:THR14 3.4 6.0 1.0
P A:PO4225 3.4 8.5 1.0
OE1 A:GLU116 3.5 7.8 1.0
O2B A:ADP222 3.5 6.3 1.0
MG A:MG224 3.6 10.3 1.0
NZ A:LYS35 3.7 7.1 1.0
N A:THR14 3.8 5.8 1.0
O3 A:PO4225 3.8 10.7 1.0
O2A A:ADP222 4.1 7.8 1.0
CA A:THR14 4.1 5.1 1.0
CB A:ASP50 4.2 6.2 1.0
O4 A:PO4225 4.2 10.6 1.0
O3B A:ADP222 4.3 6.5 1.0
O3A A:ADP222 4.3 7.5 1.0
CB A:LYS13 4.3 5.6 1.0
CE A:LYS13 4.4 7.9 1.0
CG A:GLU116 4.4 6.3 1.0
O2 A:PO4225 4.5 8.1 1.0
O A:HOH231 4.5 17.5 1.0
NZ A:LYS13 4.5 9.7 1.0
CG2 A:THR14 4.5 6.8 1.0
PA A:ADP222 4.6 7.4 1.0
CE A:LYS35 4.6 6.3 1.0
O A:HOH307 4.7 13.4 1.0
C A:LYS13 4.8 5.1 1.0
O A:HOH540 4.9 14.8 1.0

Magnesium binding site 2 out of 2 in 3qxh

Go back to Magnesium Binding Sites List in 3qxh
Magnesium binding site 2 out of 2 in the Crystal Structure of Dethiobiotin Synthetase (Biod) From Helicobacter Pylori Complexed with Adp 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 Adp and 8-Aminocaprylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg224

b:10.3
occ:1.00
O3 A:PO4225 2.0 10.7 1.0
O2B A:ADP222 2.1 6.3 1.0
O A:HOH540 2.2 14.8 1.0
O A:HOH307 2.2 13.4 1.0
O A:HOH539 2.2 13.9 1.0
O A:HOH337 2.2 7.9 1.0
P A:PO4225 3.1 8.5 1.0
O1 A:PO4225 3.2 9.1 1.0
PB A:ADP222 3.3 6.2 1.0
MG A:MG223 3.6 6.2 1.0
O1B A:ADP222 3.8 6.2 1.0
O2A A:ADP222 3.8 7.8 1.0
OG1 A:THR9 3.9 9.9 1.0
NAA A:8AC221 3.9 15.9 1.0
O2 A:PO4225 3.9 8.1 1.0
O A:HOH231 4.0 17.5 1.0
OD1 A:ASN10 4.0 14.2 0.5
O3A A:ADP222 4.1 7.5 1.0
N A:ASN10 4.3 7.0 0.5
N A:ASN10 4.3 6.9 0.5
O4 A:PO4225 4.3 10.6 1.0
O A:HOH314 4.4 28.0 1.0
OD2 A:ASP50 4.4 6.5 1.0
OD1 A:ASP50 4.4 7.7 1.0
O3B A:ADP222 4.5 6.5 1.0
PA A:ADP222 4.6 7.4 1.0
CA A:ASN10 4.6 8.0 0.5
CA A:ASN10 4.7 8.2 0.5
OD1 A:ASN10 4.7 15.4 0.5
O A:HOH576 4.8 36.3 1.0
CG A:ASN10 4.8 12.7 0.5
CG A:ASP50 4.9 6.8 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 10:12:47 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy