Manganese in PDB 5uqt: Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain Co- Crystallized with Apigenin

The structure of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain Co- Crystallized with Apigenin, PDB code: 5uqt 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)	44.44 / 2.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.090, 154.810, 271.360, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.6

The binding sites of Manganese atom in the Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain Co- Crystallized with Apigenin (pdb code 5uqt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain Co- Crystallized with Apigenin, PDB code: 5uqt:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain Co- Crystallized with Apigenin


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 Co- Crystallized with Apigenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:90.8 occ:1.00 OD2 A:ASP288 2.4 62.8 1.0 OG A:SER518 2.8 84.3 1.0 CG A:GLU515 2.9 70.9 1.0 OE2 A:GLU515 2.9 73.0 1.0 OD1 A:ASP288 3.0 57.4 1.0 CG A:ASP288 3.1 56.3 1.0 CD A:GLU515 3.4 68.9 1.0 CB A:SER518 3.8 86.6 1.0 OD2 A:ASP286 3.8 57.9 1.0 OE1 A:GLN385 3.9 60.0 1.0 CB A:GLU515 4.3 69.8 1.0 CB A:ASP288 4.5 53.9 1.0 CA A:GLU515 4.5 67.9 1.0 OE1 A:GLU515 4.6 69.4 1.0 CG A:ASP286 4.6 57.5 1.0 CB A:ASP286 4.7 53.0 1.0 O A:GLU515 4.9 66.6 1.0 CB A:GLN385 5.0 60.4 1.0

Manganese binding site 2 out of 2 in the Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain Co- Crystallized with Apigenin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Clostridium Difficile Toxin B (Tcdb) Glucosyltransferase Domain Co- Crystallized with Apigenin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:1.0 occ:1.00 OD2 B:ASP288 2.6 0.2 1.0 OG B:SER518 2.8 0.1 1.0 CG B:GLU515 2.8 0.8 1.0 OE2 B:GLU515 3.1 0.2 1.0 CG B:ASP288 3.3 0.2 1.0 CD B:GLU515 3.4 0.0 1.0 OD1 B:ASP288 3.5 0.6 1.0 CB B:SER518 3.8 0.5 1.0 OD2 B:ASP286 3.9 90.2 1.0 OE1 B:GLN385 4.0 91.4 1.0 CB B:GLU515 4.0 0.4 1.0 CA B:GLU515 4.2 0.8 1.0 O B:GLU515 4.5 0.3 1.0 OE1 B:GLU515 4.6 0.0 1.0 CB B:ASP288 4.7 0.6 1.0 CG B:ASP286 4.8 94.7 1.0 C B:GLU515 4.9 0.6 1.0 CB B:ASP286 5.0 98.7 1.0 CE B:MET289 5.0 0.6 1.0

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