Manganese in PDB 7lou: Crystal Structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine

The structure of Crystal Structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine, PDB code: 7lou was solved by R.K.Harijan, A.S.Paparella, B.L.Aboulache, J.B.Bonanno, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	104.61 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.087, 121.34, 206.417, 90, 90, 90
R / Rfree (%)	21.5 / 25.2

The binding sites of Manganese atom in the Crystal Structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine (pdb code 7lou). 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 Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine, PDB code: 7lou:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine


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 Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn612 b:31.6 occ:1.00 OD2 A:ASP288 1.9 35.0 1.0 O2B A:UDP610 2.0 30.8 1.0 O1A A:UDP610 2.1 34.5 1.0 O A:HOH710 2.2 31.7 1.0 OE1 A:GLU515 2.3 39.3 1.0 O A:HOH731 2.4 39.8 1.0 CG A:ASP288 2.9 38.9 1.0 PB A:UDP610 3.2 31.3 1.0 OD1 A:ASP288 3.2 38.4 1.0 PA A:UDP610 3.3 34.8 1.0 O3A A:UDP610 3.6 33.7 1.0 CD A:GLU515 3.6 39.5 1.0 O3B A:UDP610 3.6 32.5 1.0 O A:HOH848 3.7 43.6 1.0 O A:HOH743 3.8 36.7 1.0 O A:HOH781 4.1 30.8 1.0 O2A A:UDP610 4.1 39.2 1.0 OD2 A:ASP286 4.2 32.9 1.0 CA A:GLU515 4.2 31.6 1.0 CB A:ASP288 4.3 33.0 1.0 OE2 A:GLU515 4.3 42.6 1.0 NE2 A:GLN385 4.3 28.1 1.0 O A:GLU515 4.3 33.5 1.0 O5' A:UDP610 4.5 35.4 1.0 O1B A:UDP610 4.5 33.7 1.0 CB A:GLU515 4.6 33.0 1.0 CG A:GLU515 4.6 35.9 1.0 C A:GLU515 4.8 32.3 1.0 CB A:ASP286 4.8 32.2 1.0 CG A:ASP286 4.9 33.4 1.0 C5' A:UDP610 5.0 35.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine


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 Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Isofagomine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn613 b:34.0 occ:1.00 O2B B:UDP611 2.0 32.8 1.0 OD2 B:ASP288 2.1 36.4 1.0 O B:HOH727 2.2 33.1 1.0 O2A B:UDP611 2.2 32.6 1.0 O B:HOH759 2.2 39.2 1.0 OE1 B:GLU515 2.4 40.8 1.0 CG B:ASP288 3.0 35.6 1.0 PB B:UDP611 3.1 33.2 1.0 OD1 B:ASP288 3.3 35.5 1.0 PA B:UDP611 3.3 33.9 1.0 O3A B:UDP611 3.4 33.5 1.0 CD B:GLU515 3.6 40.1 1.0 O1B B:UDP611 3.7 35.0 1.0 O B:HOH757 3.8 44.7 1.0 O B:HOH847 3.8 37.4 1.0 O B:HOH777 4.0 28.4 1.0 OD2 B:ASP286 4.1 29.1 1.0 O1A B:UDP611 4.1 34.1 1.0 NE2 B:GLN385 4.3 29.1 1.0 OE2 B:GLU515 4.3 45.8 1.0 CA B:GLU515 4.3 34.9 1.0 O B:GLU515 4.3 35.8 1.0 CB B:ASP288 4.4 34.2 1.0 O3B B:UDP611 4.4 31.7 1.0 O5' B:UDP611 4.6 33.0 1.0 CG B:GLU515 4.7 36.1 1.0 CB B:GLU515 4.7 36.0 1.0 CG B:ASP286 4.8 31.4 1.0 CB B:ASP286 4.8 30.9 1.0 C B:GLU515 4.8 35.4 1.0 C5' B:UDP611 5.0 31.4 1.0

A.S.Paparella, B.L.Aboulache, R.K.Harijan, K.S.Potts, P.C.Tyler, V.L.Schramm. Inhibition of Clostridium Difficile Tcda and Tcdb Toxins with Transition State Analogues. Nat Commun V. 12 6285 2021.
ISSN: ESSN 2041-1723
PubMed: 34725358
DOI: 10.1038/S41467-021-26580-6