Manganese in PDB 4dmw: Crystal Structure of the Gt Domain of Clostridium Difficile Toxin A (Tcda) in Complex with Udp and Manganese

The structure of Crystal Structure of the Gt Domain of Clostridium Difficile Toxin A (Tcda) in Complex with Udp and Manganese, PDB code: 4dmw was solved by E.Malito, N.D'urzo, M.J.Bottomley, M.Biancucci, M.Scarselli, D.Maione, M.Martinelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.12 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.660, 156.730, 65.750, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.9

The binding sites of Manganese atom in the Crystal Structure of the Gt Domain of Clostridium Difficile Toxin A (Tcda) in Complex with Udp and Manganese (pdb code 4dmw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of the Gt Domain of Clostridium Difficile Toxin A (Tcda) in Complex with Udp and Manganese, PDB code: 4dmw:

Manganese binding site 1 out of 1 in the Crystal Structure of the Gt Domain of Clostridium Difficile Toxin A (Tcda) in Complex with Udp and Manganese


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 the Gt Domain of Clostridium Difficile Toxin A (Tcda) in Complex with Udp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:61.1 occ:1.00 O2B A:UDP602 2.6 70.9 1.0 O2A A:UDP602 2.6 49.0 1.0 OD2 A:ASP287 2.6 47.6 1.0 O A:HOH763 2.7 41.4 1.0 OE2 A:GLU514 3.1 49.7 1.0 O3B A:UDP602 3.3 62.2 1.0 PB A:UDP602 3.4 70.2 1.0 CG A:ASP287 3.4 39.4 1.0 OD1 A:ASP287 3.6 37.2 1.0 PA A:UDP602 3.8 56.2 1.0 CD A:GLU514 4.0 54.6 1.0 O3A A:UDP602 4.0 68.8 1.0 CG A:GLU514 4.0 47.2 1.0 CB A:SER517 4.1 58.0 1.0 O A:GLU514 4.2 52.7 1.0 CA A:GLU514 4.2 40.6 1.0 OE1 A:GLN384 4.2 31.4 1.0 O A:SER517 4.3 62.7 1.0 O A:HOH719 4.3 34.0 1.0 OD2 A:ASP285 4.4 40.2 1.0 C A:SER517 4.6 63.3 1.0 C A:GLU514 4.7 45.7 1.0 O1A A:UDP602 4.7 47.5 1.0 O1B A:UDP602 4.7 70.8 1.0 CD1 A:LEU518 4.7 59.9 1.0 CB A:GLU514 4.8 42.8 1.0 CB A:ASP287 4.8 33.9 1.0 O5' A:UDP602 4.9 52.9 1.0 C5' A:UDP602 4.9 44.7 1.0 CA A:SER517 5.0 60.3 1.0

N.D'urzo, E.Malito, M.Biancucci, M.J.Bottomley, D.Maione, M.Scarselli, M.Martinelli. The Structure of Clostridium Difficile Toxin A Glucosyltransferase Domain Bound to MN2+ and Udp Provides Insights Into Glucosyltransferase Activity and Product Release. Febs J. V. 279 3085 2012.
ISSN: ISSN 1742-464X
PubMed: 22747490
DOI: 10.1111/J.1742-4658.2012.08688.X