Magnesium in PDB 2q28: Crystal Structure of Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate

All present enzymatic activity of Crystal Structure of Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate:
4.1.1.8;

The structure of Crystal Structure of Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate, PDB code: 2q28 was solved by T.Werther, A.Zimmer, G.Wille, G.Hubner, M.S.Weiss, S.Konig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.61 / 1.74
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	132.270, 143.620, 147.580, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate (pdb code 2q28). 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 Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate, PDB code: 2q28:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate


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 Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:13.4 occ:1.00 OD1 A:ASP447 2.0 13.9 1.0 O2A A:TPP4001 2.0 11.7 1.0 O3B A:TPP4001 2.1 12.1 1.0 O A:GLY476 2.1 12.3 1.0 OD1 A:ASN474 2.2 13.0 1.0 O A:HOH4057 2.2 10.1 1.0 CG A:ASN474 3.1 13.9 1.0 PB A:TPP4001 3.2 13.6 1.0 CG A:ASP447 3.2 14.8 1.0 PA A:TPP4001 3.2 12.4 1.0 C A:GLY476 3.3 13.2 1.0 ND2 A:ASN474 3.4 13.9 1.0 O3A A:TPP4001 3.6 12.7 1.0 O2B A:TPP4001 3.8 14.4 1.0 OD2 A:ASP447 3.9 15.5 1.0 N A:ASP447 3.9 11.3 1.0 O7 A:TPP4001 3.9 12.4 1.0 N A:GLY476 4.0 14.0 1.0 O A:PHE472 4.1 13.9 1.0 N A:SER448 4.1 11.4 1.0 CA A:GLY476 4.2 13.7 1.0 N A:TYR478 4.3 13.1 1.0 N A:ILE477 4.3 12.8 1.0 CB A:ASP447 4.4 12.6 1.0 O1A A:TPP4001 4.4 11.7 1.0 CB A:ASN474 4.5 12.8 1.0 O1B A:TPP4001 4.5 12.8 1.0 N A:ASN474 4.5 12.2 1.0 CA A:ASP447 4.5 11.8 1.0 CA A:ILE477 4.5 12.2 1.0 OH A:TYR372 4.7 15.2 1.0 C A:GLY446 4.7 11.8 1.0 CA A:GLY446 4.7 11.8 1.0 C A:ASP447 4.8 11.7 1.0 C A:ILE477 4.9 12.2 1.0 CA A:ASN474 4.9 13.2 1.0 N A:GLY475 4.9 13.4 1.0 CB A:SER448 4.9 10.7 1.0 C A:ASN474 5.0 13.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate


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 Oxalyl-Coa Decarboxylase From Escherichia Coli in Complex with Adenosine-5`-Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:23.2 occ:1.00 O1B B:TPP5001 2.1 19.9 1.0 O B:GLY476 2.1 21.4 1.0 OD1 B:ASP447 2.1 20.6 1.0 O2A B:TPP5001 2.1 20.6 1.0 OD1 B:ASN474 2.1 17.6 1.0 O B:HOH5088 2.2 17.8 1.0 CG B:ASN474 3.0 18.6 1.0 PB B:TPP5001 3.2 20.1 1.0 PA B:TPP5001 3.2 18.4 1.0 CG B:ASP447 3.3 20.2 1.0 C B:GLY476 3.3 21.1 1.0 ND2 B:ASN474 3.3 18.8 1.0 O3A B:TPP5001 3.5 20.3 1.0 O2B B:TPP5001 3.7 21.7 1.0 N B:ASP447 3.9 18.1 1.0 O7 B:TPP5001 3.9 19.1 1.0 OD2 B:ASP447 3.9 24.3 1.0 N B:GLY476 4.0 20.8 1.0 CA B:GLY476 4.1 21.4 1.0 O B:PHE472 4.2 21.6 1.0 N B:TYR478 4.2 20.6 1.0 N B:SER448 4.2 18.9 1.0 N B:ILE477 4.3 20.3 1.0 CB B:ASN474 4.4 19.1 1.0 O3B B:TPP5001 4.4 20.5 1.0 CB B:ASP447 4.4 19.1 1.0 O1A B:TPP5001 4.5 16.8 1.0 CA B:ILE477 4.5 19.6 1.0 N B:ASN474 4.5 20.3 1.0 CA B:ASP447 4.5 19.5 1.0 OH B:TYR372 4.6 22.6 1.0 C B:GLY446 4.8 18.1 1.0 C B:ILE477 4.8 19.6 1.0 CA B:GLY446 4.8 18.8 1.0 CA B:ASN474 4.9 20.0 1.0 C B:ASP447 4.9 18.8 1.0 N B:GLY475 4.9 20.4 1.0 CB B:SER448 5.0 19.1 1.0 C B:TYR478 5.0 22.4 1.0

T.Werther, A.Zimmer, G.Wille, R.Golbik, M.S.Weiss, S.Konig. New Insights Into Structure-Function Relationships of Oxalyl Coa Decarboxylase From Escherichia Coli. Febs J. V. 277 2628 2010.
ISSN: ISSN 1742-464X
PubMed: 20553497
DOI: 10.1111/J.1742-464X.2010.07673.X