Manganese in PDB 3n4a: Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol

All present enzymatic activity of Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol:
5.3.1.5;

The structure of Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol, PDB code: 3n4a was solved by J.Behnen, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.94
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.290, 99.130, 102.630, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 18.2

The structure of Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol (pdb code 3n4a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol, PDB code: 3n4a:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:17.6 occ:1.00 O A:HOH2350 1.9 13.4 1.0 OE2 A:GLU216 2.0 17.6 1.0 OD1 A:ASP254 2.0 16.2 1.0 OD1 A:ASP256 2.1 21.7 1.0 CG A:ASP254 2.6 14.1 1.0 OD2 A:ASP254 2.7 15.0 1.0 NE2 A:HIS219 2.8 15.3 1.0 CD A:GLU216 2.9 15.6 1.0 CG A:ASP256 3.0 22.6 1.0 OD2 A:ASP256 3.2 29.4 1.0 OE1 A:GLU216 3.2 14.3 1.0 CD2 A:HIS219 3.3 7.9 1.0 O A:HOH2349 3.6 23.9 1.0 ND2 A:ASN246 3.8 11.3 1.0 CE1 A:HIS219 3.8 15.7 1.0 O A:HOH2133 3.9 41.4 1.0 O A:HOH2050 4.1 19.4 1.0 CB A:ASP254 4.1 14.9 1.0 CG A:GLU216 4.3 11.3 1.0 CB A:ASP256 4.4 11.3 1.0 O A:HOH2229 4.5 32.8 1.0 OD1 A:ASP286 4.5 15.9 1.0 CG A:HIS219 4.5 15.0 1.0 ND1 A:HIS219 4.7 15.8 1.0 O A:ASP286 4.8 12.8 1.0 CA A:ASP256 4.8 11.3 1.0 MN A:MN801 4.8 22.2 1.0 CG A:ASP286 4.9 16.3 1.0 N A:ASP256 4.9 15.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of D-Xylose Isomerase in Complex with S-1,2- Propandiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:22.2 occ:1.00 OD2 A:ASP244 1.9 15.8 1.0 OE1 A:GLU216 2.0 14.3 1.0 OD1 A:ASP286 2.0 15.9 1.0 OE2 A:GLU180 2.0 14.1 1.0 O2 A:PGO601 2.6 13.9 0.7 O A:HOH2133 2.8 41.4 1.0 CD A:GLU180 3.0 17.6 1.0 CG A:ASP244 3.0 11.4 1.0 CG A:ASP286 3.0 16.3 1.0 CD A:GLU216 3.2 15.6 1.0 OE1 A:GLU180 3.2 20.1 1.0 CB A:ASP286 3.4 14.0 1.0 CB A:ASP244 3.6 11.8 1.0 C2 A:PGO601 3.6 15.4 0.7 CG A:GLU216 3.9 11.3 1.0 O A:HOH2079 3.9 20.5 1.0 CB A:GLU216 3.9 11.2 1.0 C3 A:PGO601 3.9 21.8 0.7 O A:HOH2350 4.0 13.4 1.0 OD1 A:ASP244 4.1 15.7 1.0 OE2 A:GLU216 4.2 17.6 1.0 OD2 A:ASP286 4.2 13.5 1.0 CE1 A:HIS219 4.3 15.7 1.0 CG A:GLU180 4.3 16.0 1.0 NE2 A:HIS219 4.7 15.3 1.0 ND2 A:ASN214 4.8 11.6 1.0 MN A:MN701 4.8 17.6 1.0 CA A:ASP286 4.9 10.2 1.0 ND1 A:HIS219 4.9 15.8 1.0 C1 A:PGO601 4.9 23.6 0.7

J.Behnen, H.Koster, G.Neudert, T.Craan, A.Heine, G.Klebe. Experimental and Computational Active Site Mapping As A Starting Point to Fragment-Based Lead Discovery. Chemmedchem V. 7 248 2012.
ISSN: ISSN 1860-7179
PubMed: 22213702
DOI: 10.1002/CMDC.201100490