Manganese 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:

Magnesium

(Mg)

2 atoms

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

Manganese 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 Manganese with other atoms in the Mn binding site number 1 of Xylose Isomerase in 80% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:20.8 occ:1.00 OE2 A:GLU217 2.1 20.4 1.0 O A:HOH769 2.1 21.0 1.0 OD1 A:ASP257 2.2 19.7 1.0 OD2 A:ASP255 2.2 21.9 1.0 NE2 A:HIS220 2.3 17.5 1.0 OD1 A:ASP255 2.4 19.8 1.0 CG A:ASP255 2.6 21.9 1.0 CD A:GLU217 3.0 19.4 1.0 CD2 A:HIS220 3.1 17.7 1.0 CG A:ASP257 3.1 26.6 1.0 OE1 A:GLU217 3.3 19.8 1.0 OD2 A:ASP257 3.3 29.8 1.0 CE1 A:HIS220 3.4 18.9 1.0 O A:HOH802 3.9 28.1 1.0 ND2 A:ASN247 4.0 19.4 1.0 O A:HOH669 4.0 19.1 1.0 O A:HOH602 4.1 38.3 1.0 CB A:ASP255 4.1 17.2 1.0 CG A:HIS220 4.2 19.4 1.0 ND1 A:HIS220 4.3 17.9 1.0 CG A:GLU217 4.4 17.0 1.0 O A:HOH733 4.4 37.7 1.0 CB A:ASP257 4.5 17.7 1.0 CE A:LYS183 4.7 18.4 1.0 NZ A:LYS183 4.7 21.2 1.0 OD2 A:ASP287 4.8 19.6 1.0 CA A:ASP257 4.9 17.9 1.0 MG A:MG503 4.9 39.2 1.0 N A:ASP257 4.9 17.0 1.0

Manganese 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 Manganese with other atoms in the Mn binding site number 2 of Xylose Isomerase in 80% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:20.9 occ:1.00 OE2 B:GLU217 2.1 18.6 1.0 O B:HOH743 2.2 25.8 1.0 OD1 B:ASP257 2.2 19.7 1.0 OD2 B:ASP255 2.3 20.5 1.0 NE2 B:HIS220 2.3 19.1 1.0 OD1 B:ASP255 2.4 21.6 1.0 CG B:ASP255 2.7 19.0 1.0 CD2 B:HIS220 3.0 18.0 1.0 CD B:GLU217 3.1 24.2 1.0 CG B:ASP257 3.1 21.5 1.0 OE1 B:GLU217 3.3 18.8 1.0 OD2 B:ASP257 3.3 27.4 1.0 CE1 B:HIS220 3.4 19.0 1.0 O B:HOH789 3.8 28.2 1.0 ND2 B:ASN247 4.0 18.9 1.0 O B:HOH642 4.0 18.8 1.0 CB B:ASP255 4.2 15.8 1.0 CG B:HIS220 4.2 21.2 1.0 ND1 B:HIS220 4.4 18.4 1.0 CG B:GLU217 4.4 17.5 1.0 CB B:ASP257 4.5 16.6 1.0 O B:HOH791 4.6 37.0 1.0 NZ B:LYS183 4.7 24.4 1.0 CE B:LYS183 4.7 20.0 1.0 OD2 B:ASP287 4.9 19.3 1.0 CA B:ASP257 4.9 19.0 1.0 MG B:MG503 4.9 41.9 1.0 N B:ASP257 4.9 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