Magnesium in PDB 5xd8: 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: 5xd8 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)	39.14 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.487, 90.350, 104.019, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 27.7

The binding sites of Magnesium atom in the Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase (pdb code 5xd8). 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: 5xd8:
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:51.5 occ:1.00 OE2 A:GLU250 1.7 58.3 1.0 OD2 A:ASP198 2.1 61.7 1.0 OE2 A:GLU224 2.2 52.8 1.0 O A:HOH501 2.7 44.8 1.0 CD A:GLU250 2.7 47.3 1.0 CG A:ASP198 2.7 59.2 1.0 OD1 A:ASP198 2.8 58.0 1.0 CD A:GLU224 3.1 58.1 1.0 CG A:GLU224 3.3 51.8 1.0 OE1 A:GLU250 3.4 47.1 1.0 CG A:GLU250 3.6 45.0 1.0 ND2 A:ASN200 3.9 61.6 1.0 OE1 A:GLU225 3.9 57.5 1.0 CB A:ASP198 4.1 57.6 1.0 OE1 A:GLU224 4.3 53.9 1.0 CB A:GLU224 4.4 48.6 1.0 CG A:GLU225 4.5 46.0 1.0 CD A:GLU225 4.5 51.9 1.0 NZ A:LYS167 4.6 74.0 1.0 CB A:GLU225 4.7 50.1 1.0 CG A:ASN200 4.9 64.5 1.0 CB A:GLU250 4.9 41.5 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 B:Mg401 b:45.2 occ:1.00 OE2 B:GLU250 2.0 50.9 1.0 OD2 B:ASP198 2.4 40.6 1.0 OE2 B:GLU224 2.4 42.2 1.0 OD1 B:ASP198 2.6 38.5 1.0 CG B:ASP198 2.8 37.8 1.0 CG B:GLU224 3.0 36.9 1.0 CD B:GLU224 3.1 42.5 1.0 CD B:GLU250 3.1 43.8 1.0 OE1 B:GLU225 3.3 45.9 1.0 OE1 B:GLU250 3.8 45.7 1.0 ND2 B:ASN200 3.9 35.2 1.0 CG B:GLU250 4.1 46.7 1.0 CD B:GLU225 4.2 40.3 1.0 CB B:GLU225 4.2 32.7 1.0 CB B:ASP198 4.3 35.8 1.0 OE1 B:GLU224 4.3 41.0 1.0 CB B:GLU224 4.3 36.7 1.0 CG B:GLU225 4.4 32.7 1.0 CG B:ASN200 4.6 38.2 1.0 NZ B:LYS169 4.7 37.4 1.0 CA B:ASN200 4.7 35.1 1.0 N B:ASN200 4.8 27.4 1.0 O B:GLU224 4.8 27.7 1.0 C B:GLU224 4.8 32.1 1.0 NZ B:LYS167 5.0 43.0 1.0 N B:GLU225 5.0 35.5 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