Magnesium in PDB 9g5w: Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography

All present enzymatic activity of Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography:
5.3.1.5;

The structure of Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography, PDB code: 9g5w was solved by E.C.Schulz, A.Prester, D.V.Stetten, G.Gore, C.E.Hatton, K.Bartels, J.P.Leimkohl, H.Schikora, H.M.Ginn, F.Tellkamp, P.Mehrabi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.49 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.2, 103.05, 99.25, 90, 90, 90
R / Rfree (%)	17.3 / 20.7

The binding sites of Magnesium atom in the Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography (pdb code 9g5w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography, PDB code: 9g5w:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.8 occ:1.00 OE2 A:GLU181 1.9 24.6 1.0 OD2 A:ASP287 2.0 19.4 1.0 OE1 A:GLU217 2.1 15.0 1.0 OD2 A:ASP245 2.1 18.1 1.0 O A:HOH521 2.2 31.7 1.0 O A:HOH518 2.2 35.5 1.0 CD A:GLU181 2.9 21.2 1.0 CG A:ASP287 3.1 19.1 1.0 OE1 A:GLU181 3.3 25.1 1.0 CG A:ASP245 3.3 17.6 1.0 CD A:GLU217 3.3 14.0 1.0 CB A:ASP287 3.6 13.8 1.0 O A:HOH686 3.8 18.8 1.0 O A:HOH585 3.8 31.0 1.0 O A:HOH721 3.8 48.6 1.0 CB A:ASP245 3.9 15.1 1.0 CE1 A:HIS220 4.1 14.3 1.0 CG A:GLU217 4.2 13.7 1.0 OD1 A:ASP287 4.2 17.1 1.0 CB A:GLU217 4.2 15.2 1.0 CG A:GLU181 4.2 13.8 1.0 OE2 A:GLU217 4.2 14.4 1.0 OD1 A:ASP245 4.3 19.5 1.0 NE2 A:HIS220 4.7 14.8 1.0 ND1 A:HIS220 4.8 14.8 1.0 MG A:MG402 4.9 14.7 1.0 ND2 A:ASN215 4.9 17.0 1.0

Magnesium binding site 2 out of 2 in the Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xylose Isomerase Collected at 40C Using Serial Fixed-Target Crystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:14.7 occ:1.00 OE2 A:GLU217 2.0 14.4 1.0 O A:HOH686 2.0 18.8 1.0 OD2 A:ASP255 2.1 17.5 1.0 OD1 A:ASP257 2.2 16.2 1.0 NE2 A:HIS220 2.3 14.8 1.0 OD1 A:ASP255 2.4 17.5 1.0 CG A:ASP255 2.5 20.0 1.0 CD A:GLU217 3.0 14.0 1.0 CD2 A:HIS220 3.0 12.8 1.0 CG A:ASP257 3.2 17.2 1.0 OE1 A:GLU217 3.3 15.0 1.0 OD2 A:ASP257 3.4 20.6 1.0 CE1 A:HIS220 3.4 14.3 1.0 O A:HOH744 3.7 26.7 1.0 ND2 A:ASN247 4.0 12.2 1.0 CB A:ASP255 4.0 16.6 1.0 O A:HOH583 4.1 15.4 1.0 CG A:HIS220 4.2 12.7 1.0 CG A:GLU217 4.3 13.7 1.0 ND1 A:HIS220 4.4 14.8 1.0 O A:HOH521 4.5 31.7 1.0 CB A:ASP257 4.6 11.7 1.0 O A:HOH683 4.7 36.0 1.0 CE A:LYS183 4.8 18.3 1.0 OD2 A:ASP287 4.8 19.4 1.0 MG A:MG401 4.9 20.8 1.0 CA A:ASP257 4.9 13.6 1.0 N A:ASP257 5.0 13.0 1.0

E.C.Schulz, A.Prester, D.Von Stetten, G.Gore, C.E.Hatton, K.Bartels, J.P.Leimkohl, H.Schikora, H.M.Ginn, F.Tellkamp, P.Mehrabi. Probing the Modulation of Enzyme Kinetics By Multi-Temperature, Time-Resolved Serial Crystallography. Nat Commun V. 16 6553 2025.
ISSN: ESSN 2041-1723
PubMed: 40670369
DOI: 10.1038/S41467-025-61631-2