Magnesium in PDB 4qeh: Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two MG2+ Ions and L-Ribose

All present enzymatic activity of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two MG2+ Ions and L-Ribose:
5.3.1.5;

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

Resolution Low / High (Å)	20.00 / 1.55
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.922, 99.561, 103.051, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.4

The binding sites of Magnesium atom in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two MG2+ Ions and L-Ribose (pdb code 4qeh). 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 Two MG2+ Ions and L-Ribose, PDB code: 4qeh:
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 Two MG2+ Ions and L-Ribose


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 Two MG2+ Ions and L-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:70.4 occ:1.00 OD2 A:ASP255 1.9 49.9 1.0 OE2 A:GLU217 2.3 19.6 1.0 CG A:ASP255 2.4 36.0 1.0 OD1 A:ASP255 2.4 38.5 1.0 O A:HOH1001 2.5 26.1 1.0 NE2 A:HIS220 2.7 18.2 1.0 OD1 A:ASP257 2.8 31.9 1.0 CD2 A:HIS220 3.1 13.4 1.0 CD A:GLU217 3.3 17.9 1.0 O A:HOH1071 3.4 27.7 1.0 CG A:ASP257 3.7 24.0 1.0 CB A:ASP255 3.8 23.0 1.0 OE1 A:GLU217 3.9 24.1 1.0 OD2 A:ASP257 3.9 30.1 1.0 CE1 A:HIS220 3.9 20.4 1.0 ND2 A:ASN247 4.1 17.1 1.0 CG A:HIS220 4.4 11.0 1.0 O A:HOH1127 4.4 30.3 1.0 NZ A:LYS183 4.4 21.4 1.0 O3' A:32O403 4.5 21.6 1.0 CG A:GLU217 4.5 12.7 1.0 CE A:LYS183 4.5 17.0 1.0 ND1 A:HIS220 4.8 15.7 1.0 CA A:ASP255 4.9 16.7 1.0

Magnesium binding site 2 out of 2 in the Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two MG2+ Ions and L-Ribose


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 Two MG2+ Ions and L-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:20.4 occ:1.00 OE1 A:GLU217 2.0 24.1 1.0 OD2 A:ASP287 2.0 23.4 1.0 OE2 A:GLU181 2.1 25.7 1.0 OD2 A:ASP245 2.1 22.0 1.0 O2' A:32O403 2.1 23.2 1.0 O3' A:32O403 2.2 21.6 1.0 CD A:GLU181 3.0 23.8 1.0 C2' A:32O403 3.1 28.9 1.0 C3' A:32O403 3.1 22.8 1.0 CG A:ASP287 3.2 20.1 1.0 CD A:GLU217 3.2 17.9 1.0 OE1 A:GLU181 3.2 25.2 1.0 CG A:ASP245 3.3 18.3 1.0 CB A:ASP287 3.8 15.3 1.0 C4' A:32O403 3.8 27.0 1.0 O A:HOH1106 3.9 30.4 1.0 CB A:ASP245 3.9 12.4 1.0 OE2 A:GLU217 4.0 19.6 1.0 O A:HOH1001 4.0 26.1 1.0 CG A:GLU217 4.2 12.7 1.0 CE1 A:HIS220 4.2 20.4 1.0 OD1 A:ASP287 4.2 17.5 1.0 OD1 A:ASP245 4.3 19.2 1.0 CB A:GLU217 4.3 14.5 1.0 CG A:GLU181 4.3 17.4 1.0 C1' A:32O403 4.3 26.6 1.0 O4' A:32O403 4.4 30.0 1.0 NE2 A:HIS220 4.6 18.2 1.0 ND2 A:ASN215 4.8 18.0 1.0

P.Langan, A.K.Sangha, T.Wymore, J.M.Parks, Z.K.Yang, B.L.Hanson, Z.Fisher, S.A.Mason, M.P.Blakeley, V.T.Forsyth, J.P.Glusker, H.L.Carrell, J.C.Smith, D.A.Keen, D.E.Graham, A.Kovalevsky. L-Arabinose Binding, Isomerization, and Epimerization By D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Structure V. 22 1287 2014.
ISSN: ISSN 0969-2126
PubMed: 25132082
DOI: 10.1016/J.STR.2014.07.002