Magnesium in PDB 6aiy: Crystal Structure of Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions

The structure of Crystal Structure of Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions, PDB code: 6aiy was solved by J.H.Chang, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.47 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.499, 88.081, 50.040, 90.00, 114.42, 90.00
R / Rfree (%)	17 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions (pdb code 6aiy). 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 Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions, PDB code: 6aiy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions


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 Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:19.8 occ:1.00 O A:LEU254 2.0 17.5 1.0 O A:HOH607 2.1 20.4 1.0 O4P A:A3P501 2.1 24.4 1.0 OD2 A:ASP236 2.1 20.5 1.0 OE2 A:GLU253 2.1 24.1 1.0 O6P A:A3P501 2.2 23.6 1.0 P2 A:A3P501 2.7 29.4 1.0 CG A:ASP236 3.1 23.1 1.0 CD A:GLU253 3.2 25.9 1.0 C A:LEU254 3.2 19.4 1.0 OD1 A:ASP236 3.4 22.0 1.0 MG A:MG503 3.6 30.0 1.0 N A:LEU254 3.6 17.7 1.0 O5P A:A3P501 3.7 27.3 1.0 CA A:LEU254 3.9 18.5 1.0 O5' A:A3P501 3.9 29.1 1.0 OE1 A:GLU253 3.9 23.4 1.0 OE2 A:GLU192 3.9 29.8 1.0 C5' A:A3P501 4.1 33.8 1.0 O A:HOH654 4.1 22.3 1.0 CG A:GLU253 4.2 18.1 1.0 CB A:LEU254 4.2 18.1 1.0 N A:LYS255 4.3 16.3 1.0 NZ A:LYS255 4.3 24.9 1.0 O A:HOH732 4.3 25.0 1.0 CD A:LYS255 4.3 24.4 1.0 CB A:ASP236 4.4 22.1 1.0 O A:HOH670 4.4 24.9 1.0 O3P A:A3P501 4.5 35.0 1.0 CE A:LYS255 4.5 21.9 1.0 CA A:LYS255 4.7 19.2 1.0 C A:GLU253 4.7 18.0 1.0 CG A:LYS255 4.8 22.2 1.0 CD A:GLU192 4.8 31.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions


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 Dxo (E234A Mutant) in Complex with Adenosine 3', 5' Bisphosphate and Two Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:30.0 occ:1.00 O4P A:A3P501 2.0 24.4 1.0 O A:HOH710 2.1 25.3 1.0 OD1 A:ASP236 2.1 22.0 1.0 O A:HOH670 2.1 24.9 1.0 O A:HOH732 2.1 25.0 1.0 O A:HOH811 2.6 33.5 1.0 CG A:ASP236 3.1 23.1 1.0 P2 A:A3P501 3.3 29.4 1.0 OD2 A:ASP236 3.6 20.5 1.0 MG A:MG502 3.6 19.8 1.0 O5P A:A3P501 3.9 27.3 1.0 O5' A:A3P501 4.0 29.1 1.0 O A:HOH682 4.0 53.6 1.0 OE2 A:GLU192 4.0 29.8 1.0 C5' A:A3P501 4.2 33.8 1.0 OE2 A:GLU253 4.2 24.1 1.0 O A:HOH607 4.2 20.4 1.0 OE1 A:GLU253 4.3 23.4 1.0 O A:ALA234 4.4 22.5 1.0 CB A:ASP236 4.4 22.1 1.0 O6P A:A3P501 4.4 23.6 1.0 N A:ASP236 4.5 20.5 1.0 CA A:ASP236 4.6 21.7 1.0 CD A:GLU253 4.7 25.9 1.0 C A:ALA234 4.8 21.1 1.0 C A:VAL235 4.8 23.1 1.0 CB A:ALA234 4.9 27.2 1.0 CD A:GLU192 4.9 31.1 1.0 O A:HOH671 5.0 23.6 1.0

J.S.Yun, J.H.Yoon, Y.J.Choi, Y.J.Son, S.Kim, L.Tong, J.H.Chang. Molecular Mechanism For the Inhibition of Dxo By Adenosine 3',5'-Bisphosphate. Biochem. Biophys. Res. V. 504 89 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30180947
DOI: 10.1016/J.BBRC.2018.08.135