Magnesium in PDB 8awf: Xylose Isomerase in 80% Relative Humidity Environment

All present enzymatic activity of Xylose Isomerase in 80% Relative Humidity Environment:
5.3.1.5;

The structure of Xylose Isomerase in 80% Relative Humidity Environment, PDB code: 8awf was solved by P.Mehrabi, S.Sung, D.Von Stetten, A.Prester, C.E.Hatton, S.Kleine-Doepke, A.Berkes, G.Gore, J.P.Leimkohl, H.Schikora, M.Kollewe, H.Rohde, M.Wilmanns, F.Tellkamp, E.C.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.78 / 1.61
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.1, 98.75, 94.71, 90, 90, 90
R / Rfree (%)	17.9 / 20.2

The structure of Xylose Isomerase in 80% Relative Humidity Environment also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Xylose Isomerase in 80% Relative Humidity Environment (pdb code 8awf). 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 in 80% Relative Humidity Environment, PDB code: 8awf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Xylose Isomerase in 80% Relative Humidity Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xylose Isomerase in 80% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:39.2 occ:1.00 OD2 A:ASP287 1.8 19.6 1.0 OE2 A:GLU181 1.9 22.1 1.0 OD2 A:ASP245 2.1 23.6 1.0 OE1 A:GLU217 2.2 19.8 1.0 O2 A:GOL501 2.7 33.5 1.0 CD A:GLU181 2.9 24.5 1.0 CG A:ASP287 2.9 23.4 1.0 OE1 A:GLU181 3.2 27.8 1.0 CG A:ASP245 3.3 19.6 1.0 CB A:ASP287 3.4 20.5 1.0 CD A:GLU217 3.4 19.4 1.0 O A:HOH769 3.7 21.0 1.0 O A:HOH713 3.8 28.4 1.0 C2 A:GOL501 3.8 32.9 1.0 CB A:ASP245 3.9 18.7 1.0 O3 A:GOL501 3.9 41.7 1.0 OD1 A:ASP287 4.0 21.6 1.0 CG A:GLU181 4.2 22.7 1.0 CG A:GLU217 4.2 17.0 1.0 CB A:GLU217 4.2 16.9 1.0 OD1 A:ASP245 4.3 20.7 1.0 CE1 A:HIS220 4.3 18.9 1.0 OE2 A:GLU217 4.4 20.4 1.0 C3 A:GOL501 4.5 42.8 1.0 O A:HOH602 4.7 38.3 1.0 NE2 A:HIS220 4.9 17.5 1.0 CA A:ASP287 4.9 20.7 1.0 MN A:MN502 4.9 20.8 1.0 ND1 A:HIS220 4.9 17.9 1.0 ND2 A:ASN215 5.0 19.7 1.0

Magnesium binding site 2 out of 2 in the Xylose Isomerase in 80% Relative Humidity Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xylose Isomerase in 80% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:41.9 occ:1.00 OE2 B:GLU181 1.8 21.3 1.0 OD2 B:ASP287 1.8 19.3 1.0 OE1 B:GLU217 2.3 18.8 1.0 OD2 B:ASP245 2.4 25.1 1.0 O2 B:GOL501 2.5 37.2 1.0 CD B:GLU181 2.7 23.0 1.0 CG B:ASP287 3.0 22.1 1.0 OE1 B:GLU181 3.1 25.6 1.0 C2 B:GOL501 3.4 34.6 1.0 CD B:GLU217 3.5 24.2 1.0 CB B:ASP287 3.6 20.6 1.0 CG B:ASP245 3.6 19.3 1.0 O1 B:GOL501 3.6 47.6 1.0 O B:HOH743 3.6 25.8 1.0 O B:HOH662 3.7 30.4 1.0 OD1 B:ASP287 4.0 21.8 1.0 CG B:GLU181 4.0 20.2 1.0 CE1 B:HIS220 4.1 19.0 1.0 C1 B:GOL501 4.2 38.9 1.0 CB B:ASP245 4.2 17.1 1.0 CG B:GLU217 4.3 17.5 1.0 CB B:GLU217 4.4 20.1 1.0 OE2 B:GLU217 4.4 18.6 1.0 OD1 B:ASP245 4.6 20.5 1.0 NE2 B:HIS220 4.7 19.1 1.0 C3 B:GOL501 4.7 26.5 1.0 O B:HOH789 4.8 28.2 1.0 ND1 B:HIS220 4.9 18.4 1.0 MN B:MN502 4.9 20.9 1.0

P.Mehrabi, S.Sung, D.Von Stetten, A.Prester, C.E.Hatton, S.Kleine-Dopke, A.Berkes, G.Gore, J.P.Leimkohl, H.Schikora, M.Kollewe, H.Rohde, M.Wilmanns, F.Tellkamp, E.C.Schulz. Millisecond Cryo-Trapping By the Spitrobot Crystal Plunger Simplifies Time-Resolved Crystallography. Nat Commun V. 14 2365 2023.
ISSN: ESSN 2041-1723
PubMed: 37185266
DOI: 10.1038/S41467-023-37834-W