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Magnesium in PDB 5y4j: Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode

Enzymatic activity of Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode

All present enzymatic activity of Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode, PDB code: 5y4j was solved by J.E.Bae, I.J.Kim, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 1.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.614, 99.416, 102.019, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode (pdb code 5y4j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode, PDB code: 5y4j:

Magnesium binding site 1 out of 1 in 5y4j

Go back to Magnesium Binding Sites List in 5y4j
Magnesium binding site 1 out of 1 in the Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:6.0
occ:1.00
 OE2 A:GLU217 2.0 7.2 1.0
OD2 A:ASP245 2.0 8.2 1.0
OD2 A:ASP287 2.0 6.7 1.0
OE2 A:GLU181 2.1 7.5 1.0
O4 A:XYL402 2.2 7.3 1.0
O2 A:XYL402 2.2 6.6 1.0
CD A:GLU181 3.0 8.7 1.0
CG A:ASP245 3.1 7.3 1.0
CG A:ASP287 3.1 6.7 1.0
CD A:GLU217 3.2 8.7 1.0
C2 A:XYL402 3.2 6.1 1.0
OE1 A:GLU181 3.3 8.0 1.0
C4 A:XYL402 3.3 6.5 1.0
C3 A:XYL402 3.5 6.2 1.0
O3 A:XYL402 3.6 6.8 1.0
CB A:ASP287 3.7 7.0 1.0
CB A:ASP245 3.7 7.2 1.0
OE1 A:GLU217 3.8 8.2 1.0
O A:HOH804 3.9 11.7 1.0
O A:HOH602 3.9 9.8 1.0
OD1 A:ASP287 4.1 6.9 1.0
OD1 A:ASP245 4.2 8.8 1.0
CG A:GLU217 4.2 6.4 1.0
CE1 A:HIS220 4.3 7.8 1.0
CB A:GLU217 4.3 5.8 1.0
CG A:GLU181 4.3 7.7 1.0
C5 A:XYL402 4.4 8.0 1.0
C1 A:XYL402 4.5 6.6 1.0
ND2 A:ASN215 4.6 8.4 1.0
NE2 A:HIS220 4.6 7.0 1.0
O1 A:XYL402 4.9 7.8 1.0

Reference:

J.E.Bae, I.J.Kim, K.H.Nam. Crystal Structure of Glucose Isomerase in Complex with Xylitol Inhibitor in One Metal Binding Mode Biochem. Biophys. Res. V. 493 666 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28865958
DOI: 10.1016/J.BBRC.2017.08.134
Page generated: Wed Aug 13 00:36:11 2025

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