Manganese in PDB 8awc: Xylose Isomerase in 85% Relative Humidity Environment

All present enzymatic activity of Xylose Isomerase in 85% Relative Humidity Environment:
5.3.1.5;

The structure of Xylose Isomerase in 85% Relative Humidity Environment, PDB code: 8awc 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)	68.29 / 1.75
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.165, 94.506, 98.794, 90, 90, 90
R / Rfree (%)	19 / 22.9

The structure of Xylose Isomerase in 85% Relative Humidity Environment also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Xylose Isomerase in 85% Relative Humidity Environment (pdb code 8awc). 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 85% Relative Humidity Environment, PDB code: 8awc:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Xylose Isomerase in 85% 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 85% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:8.7 occ:0.73 MN A:MN403 0.0 8.7 0.7 MN A:MN403 0.7 14.1 0.3 OE2 A:GLU217 2.0 11.5 1.0 OD1 A:ASP257 2.1 15.1 1.0 OD2 A:ASP255 2.3 14.0 1.0 O A:HOH658 2.3 16.3 1.0 OD1 A:ASP255 2.3 11.1 1.0 NE2 A:HIS220 2.5 11.7 1.0 CG A:ASP255 2.6 11.7 1.0 CD A:GLU217 3.0 14.7 1.0 CG A:ASP257 3.1 20.2 1.0 CD2 A:HIS220 3.1 11.9 1.0 OE1 A:GLU217 3.4 13.0 1.0 OD2 A:ASP257 3.4 19.6 1.0 CE1 A:HIS220 3.5 12.7 1.0 ND2 A:ASN247 3.9 10.5 1.0 O A:HOH600 3.9 18.9 1.0 O A:HOH548 4.0 9.9 1.0 O A:HOH502 4.0 34.2 1.0 CB A:ASP255 4.2 7.6 1.0 CG A:HIS220 4.3 8.5 1.0 CG A:GLU217 4.4 7.9 1.0 CB A:ASP257 4.5 12.9 1.0 ND1 A:HIS220 4.5 7.3 1.0 NZ A:LYS183 4.7 16.0 1.0 CE A:LYS183 4.7 12.7 1.0 O A:HOH640 4.8 29.8 1.0 CA A:ASP257 4.8 13.4 1.0 N A:ASP257 4.8 10.7 1.0

Manganese binding site 2 out of 2 in the Xylose Isomerase in 85% 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 85% Relative Humidity Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:14.1 occ:0.27 MN A:MN403 0.0 14.1 0.3 MN A:MN403 0.7 8.7 0.7 O A:HOH658 2.0 16.3 1.0 NE2 A:HIS220 2.0 11.7 1.0 OD2 A:ASP255 2.2 14.0 1.0 OE2 A:GLU217 2.3 11.5 1.0 OD1 A:ASP255 2.7 11.1 1.0 OD1 A:ASP257 2.8 15.1 1.0 CG A:ASP255 2.8 11.7 1.0 CD2 A:HIS220 3.0 11.9 1.0 CE1 A:HIS220 3.0 12.7 1.0 CD A:GLU217 3.1 14.7 1.0 OE1 A:GLU217 3.2 13.0 1.0 O A:HOH600 3.3 18.9 1.0 CG A:ASP257 3.6 20.2 1.0 OD2 A:ASP257 3.6 19.6 1.0 O A:HOH502 3.9 34.2 1.0 ND1 A:HIS220 4.1 7.3 1.0 CG A:HIS220 4.1 8.5 1.0 NZ A:LYS183 4.2 16.0 1.0 CE A:LYS183 4.2 12.7 1.0 CB A:ASP255 4.3 7.6 1.0 ND2 A:ASN247 4.5 10.5 1.0 CG A:GLU217 4.5 7.9 1.0 O A:HOH548 4.6 9.9 1.0 CD A:LYS183 4.9 9.7 1.0 MG A:MG401 4.9 15.7 0.3 OD2 A:ASP287 4.9 18.5 1.0 O A:HOH640 4.9 29.8 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