Magnesium in PDB 2ji9: X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza-Thdp

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

The structure of X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza-Thdp, PDB code: 2ji9 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 (°)	127.721, 127.721, 152.417, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.5

The binding sites of Magnesium atom in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza-Thdp (pdb code 2ji9). 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, PDB code: 2ji9:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1555 b:26.2 occ:1.00 O22 A:TPW1554 2.0 33.2 1.0 O A:GLY481 2.0 34.1 1.0 OD1 A:ASP452 2.1 36.5 1.0 O13 A:TPW1554 2.1 30.8 1.0 OD1 A:ASN479 2.2 36.2 1.0 O A:HOH2250 2.3 29.2 1.0 C A:GLY481 3.2 35.1 1.0 CG A:ASN479 3.2 35.1 1.0 P2 A:TPW1554 3.3 33.7 1.0 CG A:ASP452 3.3 35.2 1.0 P1 A:TPW1554 3.3 30.4 1.0 ND2 A:ASN479 3.6 35.0 1.0 O11 A:TPW1554 3.7 32.8 1.0 OD2 A:ASP452 3.8 32.5 1.0 O23 A:TPW1554 3.9 33.2 1.0 O5G A:TPW1554 4.0 29.6 1.0 N A:GLY481 4.0 35.5 1.0 N A:ASP452 4.0 34.7 1.0 CA A:GLY481 4.1 34.8 1.0 N A:ILE482 4.2 34.2 1.0 N A:SER453 4.3 38.5 1.0 O A:MET477 4.3 37.6 1.0 N A:TYR483 4.3 36.3 1.0 CA A:ILE482 4.4 34.3 1.0 O21 A:TPW1554 4.4 34.2 1.0 CB A:ASP452 4.5 34.6 1.0 O12 A:TPW1554 4.6 32.1 1.0 CB A:ASN479 4.6 34.1 1.0 CA A:ASP452 4.7 35.6 1.0 C A:ILE482 4.7 35.0 1.0 N A:ASN479 4.8 35.3 1.0 OH A:TYR377 4.8 32.6 1.0 CB A:SER453 4.9 38.2 1.0 C A:GLY451 4.9 35.2 1.0 N A:GLY480 5.0 34.0 1.0 C A:ASP452 5.0 36.5 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of Oxalyl-Coa Decarboxylase in Complex with 3-Deaza-Thdp


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1555 b:36.0 occ:1.00 OD1 B:ASP452 2.0 37.5 1.0 O B:GLY481 2.0 34.0 1.0 O22 B:TPW1554 2.0 32.8 1.0 O13 B:TPW1554 2.1 33.2 1.0 OD1 B:ASN479 2.2 39.2 1.0 O B:HOH2269 2.4 29.8 1.0 CG B:ASP452 3.2 36.7 1.0 C B:GLY481 3.3 34.1 1.0 P2 B:TPW1554 3.3 34.8 1.0 CG B:ASN479 3.3 37.5 1.0 P1 B:TPW1554 3.3 33.8 1.0 O11 B:TPW1554 3.7 34.8 1.0 ND2 B:ASN479 3.7 36.5 1.0 OD2 B:ASP452 3.8 35.7 1.0 N B:ASP452 3.8 36.2 1.0 O23 B:TPW1554 3.9 36.2 1.0 N B:GLY481 4.0 35.2 1.0 O5G B:TPW1554 4.0 33.9 1.0 N B:SER453 4.1 38.0 1.0 CA B:GLY481 4.2 34.6 1.0 N B:ILE482 4.2 33.6 1.0 CB B:ASP452 4.3 37.0 1.0 N B:TYR483 4.3 34.5 1.0 O B:MET477 4.4 38.1 1.0 CA B:ILE482 4.4 33.1 1.0 CA B:ASP452 4.4 37.1 1.0 O12 B:TPW1554 4.5 35.8 1.0 O21 B:TPW1554 4.5 33.9 1.0 CB B:ASN479 4.6 35.9 1.0 C B:GLY451 4.7 36.2 1.0 C B:ILE482 4.7 33.8 1.0 C B:ASP452 4.8 37.4 1.0 N B:ASN479 4.8 36.4 1.0 CB B:SER453 4.8 38.1 1.0 OH B:TYR377 4.8 35.3 1.0 CA B:GLY451 4.9 36.1 1.0 N B:GLY480 4.9 35.7 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