Magnesium in PDB 2ji8: X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa

All present enzymatic activity of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa:
4.1.1.8;

The structure of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa, PDB code: 2ji8 was solved by C.L.Berthold, C.G.Toyota, P.Moussatche, M.D.Wood, F.Leeper, N.G.J.Richards, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.15
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.569, 127.569, 152.035, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 23.1

The binding sites of Magnesium atom in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa (pdb code 2ji8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa, PDB code: 2ji8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1567 b:26.7 occ:1.00 O3B A:TPP1566 2.0 27.7 1.0 O A:GLY481 2.0 29.6 1.0 OD1 A:ASN479 2.2 33.1 1.0 OD1 A:ASP452 2.2 30.9 1.0 O1A A:TPP1566 2.3 25.9 1.0 O A:HOH2257 2.3 27.7 1.0 PB A:TPP1566 3.2 28.3 1.0 CG A:ASN479 3.2 30.3 1.0 C A:GLY481 3.3 29.6 1.0 CG A:ASP452 3.4 30.1 1.0 PA A:TPP1566 3.4 23.7 1.0 ND2 A:ASN479 3.6 29.3 1.0 O3A A:TPP1566 3.6 27.9 1.0 O2B A:TPP1566 3.9 27.1 1.0 OD2 A:ASP452 3.9 25.9 1.0 N A:ASP452 4.0 28.1 1.0 O7 A:TPP1566 4.0 27.7 1.0 N A:GLY481 4.1 29.1 1.0 CA A:GLY481 4.2 28.7 1.0 N A:ILE482 4.2 29.4 1.0 N A:TYR483 4.3 30.9 1.0 O A:MET477 4.3 28.7 1.0 N A:SER453 4.3 31.1 1.0 O1B A:TPP1566 4.3 28.4 1.0 CA A:ILE482 4.4 29.5 1.0 CB A:ASP452 4.6 29.4 1.0 CB A:ASN479 4.6 28.5 1.0 O2A A:TPP1566 4.7 27.3 1.0 CA A:ASP452 4.7 29.5 1.0 N A:ASN479 4.7 29.7 1.0 OH A:TYR377 4.7 26.9 1.0 C A:ILE482 4.7 29.1 1.0 C A:GLY451 4.9 28.8 1.0 CA A:GLY451 4.9 27.4 1.0 CB A:SER453 5.0 30.5 1.0 N A:GLY480 5.0 26.9 1.0 CA A:ASN479 5.0 27.6 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Formyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1564 b:28.6 occ:1.00 O3B B:TPP1563 1.8 29.6 1.0 O B:GLY481 2.1 27.9 1.0 O1A B:TPP1563 2.2 30.4 1.0 OD1 B:ASN479 2.2 33.6 1.0 OD1 B:ASP452 2.2 27.9 1.0 O B:HOH2261 2.3 28.0 1.0 PB B:TPP1563 3.1 31.5 1.0 CG B:ASN479 3.2 28.3 1.0 PA B:TPP1563 3.3 29.0 1.0 C B:GLY481 3.4 29.0 1.0 ND2 B:ASN479 3.4 25.3 1.0 CG B:ASP452 3.5 27.3 1.0 O3A B:TPP1563 3.5 30.9 1.0 O2B B:TPP1563 3.6 32.1 1.0 O7 B:TPP1563 4.0 29.2 1.0 N B:ASP452 4.0 28.0 1.0 OD2 B:ASP452 4.1 26.5 1.0 N B:TYR483 4.1 27.9 1.0 N B:GLY481 4.2 29.5 1.0 O1B B:TPP1563 4.3 29.2 1.0 N B:ILE482 4.3 28.3 1.0 CA B:GLY481 4.3 29.3 1.0 O B:MET477 4.4 27.3 1.0 CA B:ILE482 4.4 28.3 1.0 N B:SER453 4.4 28.4 1.0 O2A B:TPP1563 4.5 29.7 1.0 OH B:TYR377 4.6 28.2 1.0 CB B:ASN479 4.6 27.3 1.0 CB B:ASP452 4.6 27.7 1.0 C B:ILE482 4.6 27.6 1.0 CA B:ASP452 4.7 27.6 1.0 N B:ASN479 4.8 27.8 1.0 C B:GLY451 4.8 27.0 1.0 CA B:GLY451 4.9 26.4 1.0 CA B:TYR483 4.9 29.5 1.0 C B:TYR483 4.9 29.4 1.0

C.L.Berthold, C.G.Toyota, P.Moussatche, M.D.Wood, F.Leeper, N.G.J.Richards, Y.Lindqvist. Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis By Nonoxidative Thdp-Dependent Decarboxylases Structure V. 15 853 2007.
ISSN: ISSN 0969-2126
PubMed: 17637344
DOI: 10.1016/J.STR.2007.06.001