Magnesium in PDB 8aw9: Xylose Isomerase in 75% Relative Humidity Environment

All present enzymatic activity of Xylose Isomerase in 75% Relative Humidity Environment:
5.3.1.5;

The structure of Xylose Isomerase in 75% Relative Humidity Environment, PDB code: 8aw9 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)	52.99 / 1.62
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.144, 96.591, 97.913, 90, 90, 90
R / Rfree (%)	15.5 / 19

The structure of Xylose Isomerase in 75% Relative Humidity Environment also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Xylose Isomerase in 75% Relative Humidity Environment (pdb code 8aw9). 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 75% Relative Humidity Environment, PDB code: 8aw9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Xylose Isomerase in 75% 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 75% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:35.7 occ:1.00 OD2 A:ASP287 1.9 20.4 1.0 OE2 A:GLU181 1.9 19.3 1.0 OD2 A:ASP245 2.1 15.5 1.0 OE1 A:GLU217 2.3 14.2 1.0 O2 A:GOL403 2.6 26.6 1.0 CD A:GLU181 2.9 20.6 1.0 CG A:ASP287 3.0 18.4 1.0 OE1 A:GLU181 3.3 20.2 1.0 CG A:ASP245 3.3 17.0 1.0 CB A:ASP287 3.4 15.8 1.0 CD A:GLU217 3.5 16.4 1.0 O A:HOH551 3.7 29.1 1.0 O1 A:GOL403 3.7 34.4 1.0 O A:HOH660 3.7 18.2 1.0 C2 A:GOL403 3.9 38.5 1.0 CB A:ASP245 3.9 14.3 1.0 OD1 A:ASP287 4.0 16.9 1.0 CG A:GLU181 4.2 15.0 1.0 CB A:GLU217 4.2 11.7 1.0 CG A:GLU217 4.2 15.7 1.0 CE1 A:HIS220 4.2 13.3 1.0 OD1 A:ASP245 4.3 16.2 1.0 C1 A:GOL403 4.3 41.4 1.0 OE2 A:GLU217 4.4 15.2 1.0 NE2 A:HIS220 4.8 13.3 1.0 ND1 A:HIS220 4.9 11.6 1.0 MN A:MN402 4.9 17.4 1.0 C3 A:GOL403 4.9 35.4 1.0 ND2 A:ASN215 4.9 18.8 1.0 CA A:ASP287 4.9 12.7 1.0

Magnesium binding site 2 out of 2 in the Xylose Isomerase in 75% 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 75% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:35.2 occ:1.00 OE2 B:GLU181 1.8 18.6 1.0 OD2 B:ASP287 2.0 17.5 1.0 OE1 B:GLU217 2.2 13.8 1.0 OD2 B:ASP245 2.3 18.6 1.0 O2 B:GOL403 2.7 28.7 1.0 CD B:GLU181 2.7 21.6 1.0 CG B:ASP287 3.1 13.6 1.0 OE1 B:GLU181 3.1 23.6 1.0 CG B:ASP245 3.4 16.9 1.0 CD B:GLU217 3.4 11.9 1.0 CB B:ASP287 3.6 13.7 1.0 O B:HOH557 3.6 23.8 1.0 O B:HOH670 3.7 17.1 1.0 O3 B:GOL403 3.9 34.6 1.0 C2 B:GOL403 3.9 37.5 1.0 CB B:ASP245 4.0 12.8 1.0 CG B:GLU181 4.0 16.9 1.0 CE1 B:HIS220 4.1 13.6 1.0 CB B:GLU217 4.1 13.0 1.0 OD1 B:ASP287 4.1 17.9 1.0 CG B:GLU217 4.2 8.5 1.0 C3 B:GOL403 4.3 43.0 1.0 OE2 B:GLU217 4.4 14.9 1.0 OD1 B:ASP245 4.4 12.4 1.0 NE2 B:HIS220 4.7 13.3 1.0 ND1 B:HIS220 4.8 14.7 1.0 ND2 B:ASN215 4.8 14.7 1.0 MN B:MN402 4.9 16.1 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