Manganese in PDB 5uqm: Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain in Complex with U2F

The structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain in Complex with U2F, PDB code: 5uqm was solved by J.W.Alvin, D.B.Lacy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.28 / 2.03
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.910, 61.910, 325.980, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.8

The structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain in Complex with U2F also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Manganese atom in the Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain in Complex with U2F (pdb code 5uqm). 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 Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain in Complex with U2F, PDB code: 5uqm:

Manganese binding site 1 out of 1 in the Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain in Complex with U2F


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain in Complex with U2F within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:42.7 occ:1.00 O2A A:U2F602 2.1 38.6 1.0 O A:HOH725 2.2 34.7 1.0 O A:HOH790 2.2 41.8 1.0 O2B A:U2F602 2.3 28.1 1.0 OD2 A:ASP288 2.4 25.5 1.0 OE1 A:GLU515 2.6 35.3 1.0 CG A:ASP288 3.1 25.8 1.0 OD1 A:ASP288 3.2 24.8 1.0 PB A:U2F602 3.3 28.1 1.0 PA A:U2F602 3.3 32.3 1.0 HA A:GLU515 3.3 38.4 1.0 HE21 A:GLN385 3.5 27.0 1.0 O3A A:U2F602 3.6 30.8 0.7 O A:HOH757 3.7 28.6 1.0 CD A:GLU515 3.8 36.0 1.0 O A:HOH752 3.8 36.0 1.0 O1B A:U2F602 3.8 31.2 1.0 O A:HOH733 3.9 35.3 1.0 F1 A:U2F602 3.9 31.0 0.6 O1A A:U2F602 4.0 31.3 1.0 HE3 A:MET289 4.0 36.4 1.0 HE22 A:GLN385 4.1 27.0 1.0 NE2 A:GLN385 4.2 22.5 1.0 OD2 A:ASP286 4.2 26.1 1.0 CA A:GLU515 4.2 32.0 1.0 HB3 A:ASP286 4.3 30.2 1.0 HB2 A:GLU515 4.4 42.0 1.0 H5'2 A:U2F602 4.4 29.1 0.8 OE2 A:GLU515 4.4 35.7 1.0 O5' A:U2F602 4.5 26.6 0.8 CB A:ASP288 4.6 26.4 1.0 O1 A:U2F602 4.6 30.6 0.7 CB A:GLU515 4.7 35.0 1.0 HB3 A:GLN385 4.7 24.6 1.0 HB2 A:ASP286 4.8 30.2 1.0 HB2 A:ASP288 4.8 31.6 1.0 O A:GLU515 4.8 37.1 1.0 HB2 A:GLN385 4.8 24.6 1.0 HC A:U2F602 4.8 38.9 0.3 HB3 A:ASP288 4.8 31.6 1.0 CG A:ASP286 4.8 27.1 1.0 CG A:GLU515 4.8 36.8 1.0 CB A:ASP286 4.8 25.2 1.0 C A:GLU515 4.9 35.6 1.0 CE A:MET289 4.9 30.4 1.0 C2 A:U2F602 4.9 31.9 0.5 C5' A:U2F602 5.0 24.2 0.8

J.W.Alvin, D.B.Lacy. Clostridium Difficile Toxin Glucosyltransferase Domains in Complex with A Non-Hydrolyzable Udp-Glucose Analogue. J. Struct. Biol. V. 198 203 2017.
ISSN: ESSN 1095-8657
PubMed: 28433497
DOI: 10.1016/J.JSB.2017.04.006