Magnesium in PDB 2ji6: X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza- Thdp and Oxalyl-Coa

All present enzymatic activity of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza- Thdp and Oxalyl-Coa:
4.1.1.8;

The structure of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza- Thdp and Oxalyl-Coa, PDB code: 2ji6 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 / 2.06
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.002, 127.002, 151.813, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 21.2

The binding sites of Magnesium atom in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza- Thdp and Oxalyl-Coa (pdb code 2ji6). 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 3-Deaza- Thdp and Oxalyl-Coa, PDB code: 2ji6:
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 3-Deaza- Thdp and Oxalyl-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 3-Deaza- Thdp and Oxalyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1567 b:22.6 occ:1.00 O A:GLY481 2.0 27.1 1.0 O23 A:TPW1566 2.1 22.1 1.0 OD1 A:ASP452 2.1 33.4 1.0 OD1 A:ASN479 2.1 32.7 1.0 O13 A:TPW1566 2.2 23.4 1.0 O A:HOH2374 2.4 22.3 1.0 CG A:ASN479 3.1 27.1 1.0 C A:GLY481 3.3 26.6 1.0 CG A:ASP452 3.3 30.6 1.0 P2 A:TPW1566 3.4 23.8 1.0 P1 A:TPW1566 3.4 21.1 1.0 ND2 A:ASN479 3.5 29.8 1.0 O11 A:TPW1566 3.7 22.8 1.0 OD2 A:ASP452 3.8 28.6 1.0 O5G A:TPW1566 3.9 22.9 1.0 N A:ASP452 4.0 30.6 1.0 O21 A:TPW1566 4.0 22.5 1.0 N A:GLY481 4.0 26.1 1.0 CA A:GLY481 4.1 26.3 1.0 N A:ILE482 4.2 25.8 1.0 N A:TYR483 4.3 28.4 1.0 N A:SER453 4.3 30.3 1.0 O A:MET477 4.3 29.4 1.0 CA A:ILE482 4.4 25.8 1.0 CB A:ASP452 4.5 30.2 1.0 CB A:ASN479 4.5 26.1 1.0 O22 A:TPW1566 4.5 23.0 1.0 O12 A:TPW1566 4.6 24.5 1.0 CA A:ASP452 4.6 30.2 1.0 OH A:TYR377 4.7 29.3 1.0 N A:ASN479 4.7 28.8 1.0 C A:ILE482 4.8 25.9 1.0 C A:GLY451 4.8 29.3 1.0 CB A:SER453 4.9 30.5 1.0 CA A:GLY451 4.9 29.1 1.0 N A:GLY480 4.9 25.9 1.0 CA A:ASN479 4.9 25.5 1.0 C A:ASP452 5.0 30.6 1.0 C A:ASN479 5.0 25.5 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza- Thdp and Oxalyl-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 3-Deaza- Thdp and Oxalyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1567 b:26.6 occ:1.00 O23 B:TPW1566 2.0 27.6 1.0 O B:GLY481 2.1 24.7 1.0 OD1 B:ASP452 2.1 27.9 1.0 O13 B:TPW1566 2.1 26.6 1.0 OD1 B:ASN479 2.2 29.5 1.0 O B:HOH2433 2.3 27.1 1.0 CG B:ASN479 3.1 27.1 1.0 P2 B:TPW1566 3.2 26.7 1.0 P1 B:TPW1566 3.3 25.0 1.0 CG B:ASP452 3.3 27.1 1.0 C B:GLY481 3.3 25.0 1.0 ND2 B:ASN479 3.5 25.4 1.0 O11 B:TPW1566 3.5 28.7 1.0 O21 B:TPW1566 3.6 29.1 1.0 N B:ASP452 3.9 28.3 1.0 OD2 B:ASP452 3.9 25.5 1.0 O5G B:TPW1566 4.0 27.7 1.0 N B:GLY481 4.1 25.4 1.0 O B:MET477 4.2 28.6 1.0 N B:SER453 4.2 29.7 1.0 CA B:GLY481 4.3 25.2 1.0 N B:ILE482 4.3 24.8 1.0 N B:TYR483 4.3 26.1 1.0 O22 B:TPW1566 4.4 26.6 1.0 CA B:ILE482 4.4 24.8 1.0 CB B:ASP452 4.5 29.0 1.0 O12 B:TPW1566 4.5 28.2 1.0 CB B:ASN479 4.5 25.8 1.0 OH B:TYR377 4.5 31.2 1.0 CA B:ASP452 4.6 28.5 1.0 N B:ASN479 4.7 27.5 1.0 C B:GLY451 4.7 27.4 1.0 C B:ILE482 4.8 25.0 1.0 CA B:GLY451 4.8 27.7 1.0 C B:ASP452 4.9 30.2 1.0 CB B:SER453 4.9 30.5 1.0 CA B:ASN479 5.0 26.2 1.0 N B:GLY480 5.0 25.5 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