Magnesium in PDB 4duo: Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7

All present enzymatic activity of Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7:
5.3.1.5;

The structure of Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7, PDB code: 4duo was solved by A.Y.Kovalevsky, L.Hanson, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.790, 99.620, 102.830, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 20

The binding sites of Magnesium atom in the Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7 (pdb code 4duo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7, PDB code: 4duo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:42.8 occ:1.00 OD2 A:ASP255 1.8 17.6 0.5 O A:HOH1001 2.5 17.2 1.0 CG A:ASP255 2.6 21.0 0.5 OE2 A:GLU217 2.7 13.6 1.0 OD1 A:ASP257 2.7 26.1 1.0 O1 A:XYL403 2.8 17.9 1.0 OD1 A:ASP255 2.9 27.9 0.5 NE2 A:HIS220 2.9 13.8 1.0 OD2 A:ASP255 3.3 5.2 0.6 CD2 A:HIS220 3.5 7.5 1.0 CG A:ASP257 3.5 20.7 1.0 OD2 A:ASP257 3.6 32.3 1.0 O2 A:XYL403 3.6 11.7 1.0 C1 A:XYL403 3.7 15.5 1.0 CD A:GLU217 3.7 14.7 1.0 CB A:ASP255 4.0 16.4 0.6 CB A:ASP255 4.0 15.5 0.5 CE1 A:HIS220 4.1 12.3 1.0 CG A:ASP255 4.1 14.4 0.6 NZ A:LYS183 4.2 13.3 1.0 OE1 A:GLU217 4.2 14.3 1.0 C2 A:XYL403 4.3 16.0 1.0 CE A:LYS183 4.4 12.7 1.0 ND2 A:ASN247 4.5 12.0 1.0 CG A:HIS220 4.8 10.2 1.0 O A:HOH1080 4.8 20.8 1.0 CG A:GLU217 4.9 8.5 1.0 O A:HOH1218 4.9 53.5 1.0 CB A:ASP257 5.0 13.9 1.0

Magnesium binding site 2 out of 2 in the Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Room-Temperature X-Ray Structure of D-Xylose Isomerase in Complex with 2MG2+ Ions and Xylitol at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:5.5 occ:1.00 OE1 A:GLU217 2.0 14.3 1.0 OD2 A:ASP245 2.0 13.5 1.0 OD2 A:ASP287 2.0 16.1 1.0 OE2 A:GLU181 2.1 14.3 1.0 O4 A:XYL403 2.2 9.1 1.0 O2 A:XYL403 2.2 11.7 1.0 CD A:GLU181 3.0 7.7 1.0 CG A:ASP287 3.1 16.9 1.0 CG A:ASP245 3.2 16.2 1.0 CD A:GLU217 3.2 14.7 1.0 OE1 A:GLU181 3.2 10.3 1.0 C2 A:XYL403 3.3 16.0 1.0 C4 A:XYL403 3.3 18.0 1.0 C3 A:XYL403 3.5 14.5 1.0 O3 A:XYL403 3.5 12.3 1.0 CB A:ASP287 3.6 14.9 1.0 CB A:ASP245 3.8 9.4 1.0 O A:HOH1037 3.8 24.6 1.0 OE2 A:GLU217 3.9 13.6 1.0 O A:HOH1001 4.0 17.2 1.0 CE1 A:HIS220 4.2 12.3 1.0 OD1 A:ASP287 4.2 18.2 1.0 OD1 A:ASP245 4.2 13.9 1.0 CG A:GLU217 4.2 8.5 1.0 CB A:GLU217 4.3 16.1 1.0 CG A:GLU181 4.4 12.8 1.0 NE2 A:HIS220 4.4 13.8 1.0 C5 A:XYL403 4.5 17.6 1.0 C1 A:XYL403 4.5 15.5 1.0 ND2 A:ASN215 4.8 11.5 1.0 O1 A:XYL403 4.9 17.9 1.0

A.Kovalevsky, B.L.Hanson, S.A.Mason, V.T.Forsyth, Z.Fisher, M.Mustyakimov, M.P.Blakeley, D.A.Keen, P.Langan. Inhibition of D-Xylose Isomerase By Polyols: Atomic Details By Joint X-Ray/Neutron Crystallography. Acta Crystallogr.,Sect.D V. 68 1201 2012.
ISSN: ISSN 0907-4449
PubMed: 22948921
DOI: 10.1107/S0907444912024808