Manganese in PDB 7uby: Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3

The structure of Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3, PDB code: 7uby was solved by B.Chen, J.Rongsheng, P.Kay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.57 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.118, 131.641, 83.796, 90, 110.02, 90
R / Rfree (%)	21.8 / 26.1

The binding sites of Manganese atom in the Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3 (pdb code 7uby). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3, PDB code: 7uby:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:37.6 occ:1.00 O2A B:UPG601 2.0 29.9 1.0 O1B B:UPG601 2.2 35.7 1.0 OE1 B:GLU514 2.3 33.2 1.0 O B:HOH721 2.3 28.0 1.0 OD2 B:ASP287 2.4 31.1 1.0 PB B:UPG601 3.2 38.2 1.0 PA B:UPG601 3.2 38.8 1.0 CG B:ASP287 3.3 32.7 1.0 OD1 B:ASP287 3.5 30.6 1.0 O2B B:UPG601 3.5 40.8 1.0 CD B:GLU514 3.5 35.6 1.0 O3A B:UPG601 3.6 36.7 1.0 O B:HOH776 3.7 26.8 1.0 O B:HOH773 4.0 32.1 1.0 O1A B:UPG601 4.1 33.5 1.0 OE2 B:GLU514 4.1 36.7 1.0 OE1 B:GLN384 4.2 30.9 1.0 OD2 B:ASP285 4.3 33.1 1.0 CA B:GLU514 4.3 38.8 1.0 O2' B:UPG601 4.4 35.2 1.0 O B:GLU514 4.4 39.0 1.0 O5C B:UPG601 4.5 32.7 1.0 O3B B:UPG601 4.6 36.9 0.0 CB B:ASP287 4.7 28.9 1.0 CG B:GLU514 4.7 35.3 1.0 CB B:GLU514 4.7 34.2 1.0 C B:GLU514 4.9 38.1 1.0 C5C B:UPG601 4.9 29.5 1.0

Manganese binding site 2 out of 2 in the Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Gtd Domain of Clostridium Difficile Toxin A in Complex with Vhh AH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:29.0 occ:1.00 O2A A:UPG601 2.0 25.4 1.0 OE1 A:GLU514 2.1 28.1 1.0 OD2 A:ASP287 2.1 20.9 1.0 O1B A:UPG601 2.2 30.2 1.0 O A:HOH706 2.3 26.5 1.0 O A:HOH735 2.3 30.3 1.0 CG A:ASP287 3.1 28.9 1.0 PB A:UPG601 3.2 39.0 1.0 PA A:UPG601 3.3 33.2 1.0 CD A:GLU514 3.3 30.7 1.0 OD1 A:ASP287 3.4 25.2 1.0 O A:HOH814 3.6 16.4 1.0 O3A A:UPG601 3.6 34.4 1.0 O2B A:UPG601 3.7 34.9 1.0 OE2 A:GLU514 3.9 35.8 1.0 O A:HOH724 4.0 29.1 1.0 O1A A:UPG601 4.1 31.2 1.0 CA A:GLU514 4.1 27.3 1.0 OD2 A:ASP285 4.2 27.4 1.0 O A:GLU514 4.2 36.3 1.0 NE2 A:GLN384 4.2 22.3 1.0 O2' A:UPG601 4.4 33.4 0.8 CG A:GLU514 4.4 27.6 1.0 CB A:GLU514 4.5 28.7 1.0 CB A:ASP287 4.5 27.5 1.0 O5C A:UPG601 4.5 30.9 1.0 O3B A:UPG601 4.5 38.7 1.0 C A:GLU514 4.7 34.9 1.0 C5C A:UPG601 4.9 30.6 1.0 CG A:ASP285 4.9 21.9 1.0 O A:GLN513 5.0 35.7 1.0 CB A:ASP285 5.0 20.6 1.0

B.Chen, K.Perry, R.Jin. Neutralizing Epitopes on Clostridioides Difficile Toxin A Revealed By the Structures of Two Camelid Vhh Antibodies. Front Immunol V. 13 78858 2022.
ISSN: ESSN 1664-3224
PubMed: 36466927
DOI: 10.3389/FIMMU.2022.978858