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

The structure of Crystal Structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Noeuromycin, PDB code: 7lov 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)	28.97 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.589, 82.676, 113.227, 90, 92.43, 90
R / Rfree (%)	20.8 / 24.8

The binding sites of Manganese atom in the Crystal Structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase in Complex with Udp and Noeuromycin (pdb code 7lov). 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 Noeuromycin, PDB code: 7lov:
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 Noeuromycin


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 Noeuromycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn606 b:28.9 occ:1.00 O2B A:UDP602 1.9 24.7 1.0 OD2 A:ASP288 2.1 28.2 1.0 O A:HOH708 2.1 32.0 1.0 O1A A:UDP602 2.2 27.3 1.0 OE1 A:GLU515 2.2 31.9 1.0 O A:HOH733 2.3 25.1 1.0 CG A:ASP288 3.1 30.0 1.0 PB A:UDP602 3.1 25.5 1.0 CD A:GLU515 3.2 32.0 1.0 PA A:UDP602 3.4 27.7 1.0 OD1 A:ASP288 3.4 31.9 1.0 O3A A:UDP602 3.6 26.3 1.0 O3B A:UDP602 3.6 24.2 1.0 OE2 A:GLU515 3.7 32.4 1.0 O A:HOH759 3.9 24.0 1.0 OD2 A:ASP286 4.0 29.4 1.0 NE2 A:GLN385 4.1 25.0 1.0 O2A A:UDP602 4.2 28.1 1.0 CA A:GLU515 4.2 31.5 1.0 O2 A:NOY601 4.2 30.7 1.0 O A:GLU515 4.2 35.2 1.0 O A:HOH755 4.2 25.9 1.0 O1B A:UDP602 4.4 24.0 1.0 CB A:ASP288 4.4 29.1 1.0 CG A:GLU515 4.5 32.3 1.0 CB A:GLU515 4.6 31.7 1.0 O5' A:UDP602 4.7 26.4 1.0 C A:GLU515 4.7 32.8 1.0 CG A:ASP286 4.8 30.0 1.0 CB A:ASP286 4.9 30.6 1.0 C5' A:UDP602 5.0 26.1 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 Noeuromycin


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 Noeuromycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn605 b:27.7 occ:1.00 OD2 B:ASP288 2.0 31.5 1.0 OE1 B:GLU515 2.1 37.5 1.0 O3B B:UDP602 2.2 28.3 1.0 O B:HOH709 2.2 23.2 1.0 O B:HOH718 2.2 22.4 1.0 O1A B:UDP602 2.2 28.5 1.0 CG B:ASP288 3.0 32.3 1.0 CD B:GLU515 3.2 35.2 1.0 OD1 B:ASP288 3.3 33.5 1.0 PB B:UDP602 3.3 29.1 1.0 PA B:UDP602 3.4 30.4 1.0 O B:HOH741 3.6 17.2 1.0 O1B B:UDP602 3.7 27.0 1.0 OE2 B:GLU515 3.7 35.0 1.0 O3A B:UDP602 3.7 29.7 1.0 OD2 B:ASP286 4.0 34.2 1.0 CA B:GLU515 4.1 33.6 1.0 NE2 B:GLN385 4.1 27.2 1.0 O B:HOH756 4.2 32.6 1.0 O B:GLU515 4.2 33.7 1.0 O2A B:UDP602 4.2 30.7 1.0 O2 B:NOY601 4.3 33.7 1.0 CB B:ASP288 4.3 31.2 1.0 CG B:GLU515 4.4 34.3 1.0 CB B:GLU515 4.5 33.8 1.0 O5' B:UDP602 4.6 31.0 1.0 O2B B:UDP602 4.7 26.2 1.0 C B:GLU515 4.7 34.8 1.0 CG B:ASP286 4.8 33.7 1.0 C5' B:UDP602 4.8 30.3 1.0 CB B:ASP286 4.9 32.3 1.0 CE B:MET289 4.9 30.9 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