Magnesium in PDB 4qe5: Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two MG2+ Ions and L-Ribulose

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

The structure of Room Temperature X-Ray Structure of D-Xylose Isomerase in Complex with Two MG2+ Ions and L-Ribulose, PDB code: 4qe5 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 / 1.56
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.928, 99.687, 103.030, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.8

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-Ribulose (pdb code 4qe5). 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-Ribulose, PDB code: 4qe5:
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-Ribulose


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-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:24.2 occ:1.00 OD2 A:ASP287 2.0 22.1 1.0 OE1 A:GLU217 2.0 28.5 1.0 O2 A:RUU403 2.1 28.4 1.0 O3 A:RUU403 2.1 24.1 1.0 OD2 A:ASP245 2.1 23.4 1.0 OE2 A:GLU181 2.2 41.3 1.0 CD A:GLU181 2.9 24.8 1.0 OE1 A:GLU181 3.0 33.5 1.0 C3 A:RUU403 3.0 31.4 1.0 C2 A:RUU403 3.1 39.5 1.0 CG A:ASP287 3.1 18.6 1.0 CD A:GLU217 3.2 20.0 1.0 CG A:ASP245 3.3 19.1 1.0 O A:HOH1099 3.7 32.8 1.0 CB A:ASP287 3.8 13.1 1.0 OE2 A:GLU217 3.9 19.4 1.0 O5 A:RUU403 3.9 34.4 1.0 CB A:ASP245 4.0 12.4 1.0 O A:HOH1001 4.1 30.6 1.0 OD1 A:ASP287 4.1 16.4 1.0 C5 A:RUU403 4.2 42.1 1.0 C4 A:RUU403 4.2 40.3 1.0 CG A:GLU181 4.3 18.3 1.0 OD1 A:ASP245 4.3 19.7 1.0 CG A:GLU217 4.3 12.4 1.0 C1 A:RUU403 4.3 30.6 1.0 CE1 A:HIS220 4.3 18.5 1.0 CB A:GLU217 4.4 13.8 1.0 O4 A:RUU403 4.5 60.5 1.0 NE2 A:HIS220 4.7 18.2 1.0 ND2 A:ASN215 4.8 18.8 1.0 MG A:MG402 4.9 59.3 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-Ribulose


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-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:59.3 occ:1.00 OD2 A:ASP255 1.9 42.7 1.0 O A:HOH1001 1.9 30.6 1.0 OE2 A:GLU217 2.3 19.4 1.0 NE2 A:HIS220 2.5 18.2 1.0 OD1 A:ASP257 2.8 30.3 1.0 CG A:ASP255 2.8 41.4 1.0 O A:HOH1131 3.0 40.2 1.0 OD1 A:ASP255 3.1 39.4 1.0 CD2 A:HIS220 3.1 14.1 1.0 O A:HOH1184 3.2 29.9 1.0 CD A:GLU217 3.3 20.0 1.0 CE1 A:HIS220 3.6 18.5 1.0 CG A:ASP257 3.7 26.8 1.0 OD2 A:ASP257 3.7 32.4 1.0 OE1 A:GLU217 3.8 28.5 1.0 O3 A:RUU403 4.1 24.1 1.0 CB A:ASP255 4.2 22.0 1.0 O4 A:RUU403 4.2 60.5 1.0 ND2 A:ASN247 4.3 18.8 1.0 CG A:HIS220 4.4 11.0 1.0 NZ A:LYS183 4.5 21.1 1.0 CG A:GLU217 4.5 12.4 1.0 CE A:LYS183 4.5 18.5 1.0 ND1 A:HIS220 4.6 14.8 1.0 OD2 A:ASP287 4.6 22.1 1.0 O A:HOH1241 4.9 49.0 1.0 MG A:MG401 4.9 24.2 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