Magnesium in PDB 2jib: X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Coenzyme-A

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

The structure of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Coenzyme-A, PDB code: 2jib 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)	30.00 / 2.2
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.662, 127.662, 152.074, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.8

The binding sites of Magnesium atom in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with Coenzyme-A (pdb code 2jib). 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 Coenzyme-A, PDB code: 2jib:
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 Coenzyme-A


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 Coenzyme-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1567 b:28.7 occ:1.00 O A:GLY481 2.0 32.3 1.0 OD1 A:ASP452 2.1 32.8 1.0 O3B A:TPP1566 2.2 30.5 1.0 O1A A:TPP1566 2.2 31.7 1.0 O A:HOH2330 2.2 35.6 1.0 OD1 A:ASN479 2.3 35.0 1.0 CG A:ASN479 3.2 33.1 1.0 C A:GLY481 3.2 32.3 1.0 CG A:ASP452 3.3 32.6 1.0 PB A:TPP1566 3.4 32.3 1.0 PA A:TPP1566 3.4 32.4 1.0 ND2 A:ASN479 3.5 32.7 1.0 O3A A:TPP1566 3.8 32.8 1.0 OD2 A:ASP452 3.9 30.7 1.0 O2B A:TPP1566 4.0 33.3 1.0 O7 A:TPP1566 4.0 31.4 1.0 N A:ASP452 4.0 32.6 1.0 N A:GLY481 4.1 32.3 1.0 N A:TYR483 4.1 32.1 1.0 N A:ILE482 4.2 32.1 1.0 CA A:GLY481 4.2 32.3 1.0 CA A:ILE482 4.3 32.0 1.0 N A:SER453 4.3 33.1 1.0 O A:MET477 4.4 32.0 1.0 CB A:ASP452 4.5 32.6 1.0 C A:ILE482 4.5 32.0 1.0 O1B A:TPP1566 4.6 32.1 1.0 CB A:ASN479 4.6 32.4 1.0 CA A:ASP452 4.6 32.8 1.0 O2A A:TPP1566 4.7 32.6 1.0 OH A:TYR377 4.8 31.9 1.0 N A:ASN479 4.8 32.2 1.0 CA A:TYR483 4.9 32.3 1.0 N A:GLY480 4.9 32.3 1.0 C A:TYR483 4.9 32.5 1.0 C A:GLY451 4.9 32.3 1.0 CB A:SER453 5.0 33.2 1.0 CA A:GLY451 5.0 32.3 1.0 O A:TYR483 5.0 32.5 1.0 C A:ASP452 5.0 33.0 1.0

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


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 Coenzyme-A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1567 b:23.8 occ:1.00 O3B B:TPP1566 2.0 32.3 1.0 OD1 B:ASN479 2.1 33.9 1.0 O B:GLY481 2.1 32.9 1.0 OD1 B:ASP452 2.2 32.9 1.0 O B:HOH2273 2.3 23.4 1.0 O1A B:TPP1566 2.4 31.4 1.0 CG B:ASN479 3.1 32.2 1.0 PB B:TPP1566 3.3 32.1 1.0 CG B:ASP452 3.3 32.8 1.0 C B:GLY481 3.3 32.9 1.0 PA B:TPP1566 3.5 30.7 1.0 ND2 B:ASN479 3.5 31.8 1.0 O2B B:TPP1566 3.7 32.2 1.0 O3A B:TPP1566 3.7 31.4 1.0 OD2 B:ASP452 3.8 31.7 1.0 N B:GLY481 4.1 32.6 1.0 O7 B:TPP1566 4.1 31.2 1.0 N B:TYR483 4.2 33.5 1.0 N B:ASP452 4.2 32.5 1.0 O B:MET477 4.2 31.1 1.0 CA B:GLY481 4.3 32.7 1.0 N B:ILE482 4.3 33.0 1.0 CA B:ILE482 4.4 33.1 1.0 O1B B:TPP1566 4.5 30.9 1.0 CB B:ASN479 4.5 31.6 1.0 N B:SER453 4.5 33.4 1.0 OH B:TYR377 4.6 30.6 1.0 CB B:ASP452 4.6 32.8 1.0 N B:ASN479 4.6 31.6 1.0 C B:ILE482 4.7 33.2 1.0 O2A B:TPP1566 4.8 31.5 1.0 C B:TYR483 4.8 33.6 1.0 N B:GLY480 4.8 31.9 1.0 CA B:ASP452 4.8 32.7 1.0 O B:TYR483 4.9 34.0 1.0 CA B:TYR483 4.9 33.5 1.0 CA B:ASN479 4.9 31.7 1.0 C B:ASN479 4.9 31.7 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