Manganese 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:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Xylose Isomerase in 75% Relative Humidity Environment (pdb code 8aw9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Xylose Isomerase in 75% Relative Humidity Environment, PDB code: 8aw9:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn binding site number 1 of Xylose Isomerase in 75% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:17.4 occ:1.00 OE2 A:GLU217 2.1 15.2 1.0 O A:HOH660 2.1 18.2 1.0 OD1 A:ASP257 2.3 18.1 1.0 OD2 A:ASP255 2.3 16.3 1.0 OD1 A:ASP255 2.4 12.3 1.0 NE2 A:HIS220 2.5 13.3 1.0 CG A:ASP255 2.7 13.9 1.0 CD A:GLU217 3.0 16.4 1.0 CD2 A:HIS220 3.1 15.0 1.0 OE1 A:GLU217 3.2 14.2 1.0 CG A:ASP257 3.2 15.6 1.0 OD2 A:ASP257 3.4 25.2 1.0 CE1 A:HIS220 3.5 13.3 1.0 ND2 A:ASN247 4.0 16.6 1.0 O A:HOH658 4.0 26.8 1.0 O A:HOH558 4.0 16.6 1.0 CB A:ASP255 4.1 16.1 1.0 CG A:HIS220 4.3 14.6 1.0 CG A:GLU217 4.4 15.7 1.0 ND1 A:HIS220 4.4 11.6 1.0 O A:HOH552 4.5 33.9 1.0 CB A:ASP257 4.6 12.7 1.0 CE A:LYS183 4.7 12.8 1.0 NZ A:LYS183 4.8 17.3 1.0 MG A:MG401 4.9 35.7 1.0 CA A:ASP257 5.0 16.5 1.0

Manganese 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 Manganese with other atoms in the Mn binding site number 2 of Xylose Isomerase in 75% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:16.1 occ:1.00 OE2 B:GLU217 2.1 14.9 1.0 O B:HOH670 2.1 17.1 1.0 OD1 B:ASP257 2.2 14.3 1.0 OD2 B:ASP255 2.3 15.3 1.0 OD1 B:ASP255 2.4 12.7 1.0 NE2 B:HIS220 2.4 13.3 1.0 CG B:ASP255 2.7 16.7 1.0 CD B:GLU217 3.0 11.9 1.0 CD2 B:HIS220 3.1 11.8 1.0 CG B:ASP257 3.1 22.7 1.0 OE1 B:GLU217 3.3 13.8 1.0 OD2 B:ASP257 3.4 22.0 1.0 CE1 B:HIS220 3.5 13.6 1.0 O B:HOH669 3.9 25.1 1.0 ND2 B:ASN247 4.0 16.3 1.0 O B:HOH526 4.1 13.5 1.0 CB B:ASP255 4.2 10.6 1.0 CG B:HIS220 4.3 16.8 1.0 CG B:GLU217 4.4 8.5 1.0 ND1 B:HIS220 4.4 14.7 1.0 CB B:ASP257 4.6 17.1 1.0 O B:HOH634 4.6 27.4 1.0 CE B:LYS183 4.7 12.4 1.0 NZ B:LYS183 4.7 15.8 1.0 CA B:ASP257 4.9 14.9 1.0 MG B:MG401 4.9 35.2 1.0 N B:ASP257 4.9 13.2 1.0 OD2 B:ASP287 5.0 17.5 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