Magnesium in PDB 5xd9: Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase

All present enzymatic activity of Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase:
5.5.1.25;

The structure of Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase, PDB code: 5xd9 was solved by S.Lee, I.-G.Choi, H.-Y.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.41 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.821, 89.821, 142.467, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 23.3

The binding sites of Magnesium atom in the Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase (pdb code 5xd9). 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 Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase, PDB code: 5xd9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:49.7 occ:1.00 OD2 A:ASP198 2.2 44.9 1.0 OE2 A:GLU224 2.3 44.1 1.0 OE1 A:GLU225 2.6 45.9 1.0 OD1 A:ASP198 2.7 39.6 1.0 CG A:ASP198 2.8 40.5 1.0 CD A:GLU224 3.1 39.8 1.0 OE1 A:GLU250 3.4 60.5 1.0 ND2 A:ASN200 3.5 47.1 1.0 CD A:GLU225 3.6 53.2 1.0 CG A:GLU224 3.7 32.3 1.0 ND2 A:ASN300 3.8 48.0 1.0 CG A:GLU225 4.0 40.4 1.0 OE1 A:GLU224 4.0 33.7 1.0 NZ A:LYS169 4.1 49.2 1.0 CB A:ASP198 4.2 27.9 1.0 CG A:ASN200 4.2 44.7 1.0 O A:HOH508 4.5 40.4 1.0 NZ A:LYS167 4.6 31.7 1.0 OD1 A:ASN200 4.6 40.1 1.0 CD A:GLU250 4.6 57.4 1.0 CB A:GLU224 4.6 28.6 1.0 CB A:GLU225 4.6 31.6 1.0 OE2 A:GLU225 4.8 49.9 1.0 CA A:ASN200 4.8 33.9 1.0 N A:ASN200 4.9 31.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:55.0 occ:1.00 OD2 A:ASP273 1.9 48.1 1.0 OE2 A:GLU250 2.7 53.5 1.0 CG A:GLU250 2.9 52.6 1.0 OH A:TYR52 2.9 43.6 1.0 CG A:ASP273 3.0 40.6 1.0 CD A:GLU250 3.2 57.4 1.0 O A:ASN300 3.6 40.9 1.0 CB A:ASP273 3.8 34.4 1.0 OD1 A:ASP273 4.0 41.5 1.0 CB A:GLU250 4.0 43.1 1.0 C A:ASN300 4.0 38.8 1.0 CZ A:TYR52 4.1 44.4 1.0 ND2 A:ASN276 4.1 38.7 1.0 CB A:ASN300 4.1 38.2 1.0 OE1 A:GLU250 4.4 60.5 1.0 O A:GLU250 4.5 47.0 1.0 N A:GLY301 4.5 34.0 1.0 CA A:GLU250 4.6 40.2 1.0 O A:HOH504 4.6 34.3 1.0 CA A:GLY301 4.6 33.5 1.0 CA A:ASN300 4.6 36.8 1.0 CE1 A:TYR52 4.7 39.6 1.0 OG A:SER275 4.8 41.5 1.0 C A:GLU250 4.9 43.1 1.0 CE2 A:TYR52 5.0 40.1 1.0

S.Lee, K.H.Kim, H.-Y.Kim, I.-G.Choi. Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase Suggests Emergence of Novel Substrate Specificity in the Enolase Superfamily Biochem. Biophys. Res. V. 491 217 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28716734
DOI: 10.1016/J.BBRC.2017.07.080