Magnesium in PDB 5xd7: 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: 5xd7 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)	37.68 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.336, 87.336, 143.069, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.8

The binding sites of Magnesium atom in the Crystal Structure Analysis of 3,6-Anhydro-L-Galactonate Cycloisomerase (pdb code 5xd7). 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: 5xd7:
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:26.7 occ:0.00 O A:THR242 2.3 29.1 1.0 O A:ALA239 2.4 24.7 1.0 C A:ALA239 3.4 24.9 1.0 C A:THR242 3.5 23.4 1.0 CA A:ALA239 4.0 24.3 1.0 N A:THR242 4.3 26.3 1.0 N A:ALA243 4.4 26.1 1.0 CB A:ALA239 4.4 17.0 1.0 CA A:ALA243 4.4 29.6 1.0 O A:HOH646 4.4 33.0 1.0 CA A:THR242 4.4 25.1 1.0 OG1 A:THR242 4.5 27.2 1.0 N A:ASP240 4.5 23.8 1.0 CA A:ASP240 4.9 22.9 1.0 C A:ALA243 4.9 26.6 1.0 C A:ASP240 5.0 26.1 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:33.9 occ:1.00 OE1 A:GLU250 2.3 25.3 1.0 OD2 A:ASP198 2.3 23.0 1.0 O A:HOH508 2.3 31.0 1.0 O A:HOH586 2.4 28.0 1.0 OE2 A:GLU224 2.4 21.3 1.0 CD A:GLU250 3.3 28.0 1.0 CG A:ASP198 3.4 22.3 1.0 CD A:GLU224 3.4 22.3 1.0 OE2 A:GLU250 3.5 26.7 1.0 NZ A:LYS167 3.6 20.1 1.0 O A:ACY403 3.7 51.6 1.0 NZ A:LYS169 3.7 28.9 1.0 OD1 A:ASP198 3.7 27.8 1.0 O A:HOH575 4.1 25.5 1.0 CG A:GLU224 4.1 19.3 1.0 OE1 A:GLU225 4.1 30.8 1.0 ND2 A:ASN200 4.2 33.6 1.0 C A:ACY403 4.3 44.4 1.0 OE1 A:GLU224 4.3 22.0 1.0 CD2 A:HIS300 4.3 23.4 1.0 O A:HOH578 4.5 32.3 1.0 H3 A:ACY403 4.6 45.2 1.0 CG A:GLU250 4.6 24.3 1.0 CB A:ASP198 4.6 18.6 1.0 H1 A:ACY403 4.7 45.2 1.0 CH3 A:ACY403 4.8 37.6 1.0 NE2 A:HIS300 4.8 21.8 1.0 CE A:LYS167 4.8 19.9 1.0 OXT A:ACY403 4.9 24.4 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