Calcium in PDB 9mui: C. Difficile RBD1 with CA2+

The structure of C. Difficile RBD1 with CA2+, PDB code: 9mui was solved by D.Hunter, E.Pozharski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.91 / 2.29
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	119.697, 119.697, 125.091, 90, 90, 120
R / Rfree (%)	19.9 / 23.4

The binding sites of Calcium atom in the C. Difficile RBD1 with CA2+ (pdb code 9mui). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the C. Difficile RBD1 with CA2+, PDB code: 9mui:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the C. Difficile RBD1 with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C. Difficile RBD1 with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:37.8 occ:1.00 O A:HOH907 2.2 37.5 1.0 O A:SER646 2.3 39.0 1.0 O A:ASN621 2.4 38.1 1.0 O A:GLN644 2.4 45.2 1.0 OD2 A:ASP734 2.4 39.0 1.0 OD2 A:ASP623 2.5 39.7 1.0 OD1 A:ASP734 2.7 35.6 1.0 CG A:ASP734 2.9 38.5 1.0 C A:SER646 3.5 40.5 1.0 CG A:ASP623 3.5 42.3 1.0 C A:ASN621 3.5 36.0 1.0 C A:GLN644 3.6 41.4 1.0 N A:SER646 3.8 37.2 1.0 OD1 A:ASP623 4.0 40.1 1.0 OD1 A:ASN735 4.1 38.4 1.0 C A:GLY645 4.2 40.7 1.0 CB A:ASN621 4.2 37.2 1.0 CA A:ASN621 4.2 36.9 1.0 N A:GLN644 4.2 42.6 1.0 CA A:SER646 4.2 37.9 1.0 CA A:GLY642 4.4 39.7 1.0 CB A:ASP734 4.4 37.5 1.0 CA A:GLY645 4.5 39.6 1.0 CA A:GLN644 4.5 41.4 0.5 CA A:GLN644 4.5 41.6 0.5 N A:ALA647 4.5 41.3 1.0 N A:GLY645 4.5 41.0 1.0 N A:PHE622 4.5 34.2 1.0 CB A:ASP623 4.6 37.0 1.0 CB A:PHE622 4.6 36.9 1.0 C A:PHE622 4.7 37.1 1.0 N A:LEU643 4.7 39.2 1.0 N A:ASP623 4.8 37.9 1.0 CA A:PHE622 4.8 32.7 1.0 CA A:ALA647 4.8 36.1 1.0 O A:GLY645 4.9 38.4 1.0 C A:GLY642 4.9 41.8 1.0 OE1 A:GLN644 5.0 44.2 0.5 CB A:GLN644 5.0 43.1 0.5 O A:PHE622 5.0 35.9 1.0

Calcium binding site 2 out of 4 in the C. Difficile RBD1 with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C. Difficile RBD1 with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:37.4 occ:1.00 O B:ASN621 2.3 34.9 1.0 O B:SER646 2.4 36.0 1.0 O B:HOH902 2.4 52.5 1.0 O B:GLN644 2.4 41.9 1.0 OD2 B:ASP734 2.5 39.5 1.0 OD2 B:ASP623 2.6 39.0 1.0 OD1 B:ASP734 2.6 37.6 1.0 CG B:ASP734 2.9 40.0 1.0 C B:ASN621 3.5 35.8 1.0 CG B:ASP623 3.5 40.4 1.0 C B:SER646 3.5 39.5 1.0 C B:GLN644 3.6 40.7 1.0 N B:SER646 3.9 33.4 1.0 OD1 B:ASP623 4.0 38.3 1.0 OD1 B:ASN735 4.1 40.8 1.0 CB B:ASN621 4.2 36.4 1.0 CA B:ASN621 4.2 38.2 1.0 C B:GLY645 4.2 39.4 1.0 N B:GLN644 4.3 47.5 1.0 CA B:SER646 4.3 38.6 1.0 CA B:GLY642 4.4 40.8 1.0 CB B:ASP734 4.4 34.0 1.0 CA B:GLY645 4.5 36.9 1.0 N B:PHE622 4.5 32.3 1.0 N B:GLY645 4.5 39.5 1.0 CA B:GLN644 4.6 40.4 1.0 N B:ALA647 4.6 40.0 1.0 CB B:PHE622 4.6 35.7 1.0 CB B:ASP623 4.6 36.7 1.0 C B:PHE622 4.7 37.8 1.0 N B:LEU643 4.7 41.4 1.0 N B:ASP623 4.7 35.4 1.0 CA B:PHE622 4.8 35.0 1.0 O B:GLY645 4.8 39.9 1.0 CA B:ALA647 4.9 34.6 1.0 OE1 B:GLN644 4.9 58.6 1.0 C B:GLY642 4.9 41.4 1.0 CG B:ASN621 5.0 36.7 1.0

Calcium binding site 3 out of 4 in the C. Difficile RBD1 with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C. Difficile RBD1 with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:43.5 occ:1.00 O C:SER646 2.3 38.2 1.0 O C:ASN621 2.3 36.0 1.0 O C:GLN644 2.4 46.1 1.0 O C:HOH908 2.4 49.5 1.0 OD2 C:ASP623 2.4 40.4 1.0 OD2 C:ASP734 2.6 43.2 1.0 OD1 C:ASP734 2.7 39.4 1.0 CG C:ASP734 3.0 41.6 1.0 CG C:ASP623 3.4 41.6 1.0 C C:SER646 3.5 42.7 1.0 C C:ASN621 3.5 37.6 1.0 C C:GLN644 3.6 43.8 1.0 N C:SER646 3.7 42.4 1.0 OD1 C:ASP623 4.0 45.3 1.0 C C:GLY645 4.1 43.3 1.0 CA C:SER646 4.2 43.8 1.0 CB C:ASN621 4.2 36.7 1.0 CA C:ASN621 4.2 37.3 1.0 OD1 C:ASN735 4.3 42.9 1.0 N C:GLN644 4.3 47.3 1.0 CA C:GLY645 4.4 39.6 1.0 CA C:GLY642 4.4 42.8 1.0 N C:GLY645 4.5 41.9 1.0 CA C:GLN644 4.5 41.3 1.0 CB C:ASP734 4.5 34.5 1.0 CB C:PHE622 4.5 38.0 1.0 N C:ALA647 4.5 40.9 1.0 CB C:ASP623 4.6 35.2 1.0 N C:PHE622 4.6 37.2 1.0 C C:PHE622 4.6 40.5 1.0 N C:ASP623 4.8 40.0 1.0 N C:LEU643 4.8 43.2 1.0 O C:GLY645 4.8 40.7 1.0 CA C:PHE622 4.8 38.0 1.0 CA C:ALA647 4.9 40.8 1.0 O C:PHE622 4.9 40.4 1.0 CB C:GLN644 4.9 40.9 1.0 C C:GLY642 5.0 45.4 1.0 CB C:SER646 5.0 44.2 1.0

Calcium binding site 4 out of 4 in the C. Difficile RBD1 with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C. Difficile RBD1 with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:46.3 occ:1.00 O D:SER646 2.3 44.9 1.0 O D:ASN621 2.3 40.6 1.0 O D:HOH903 2.4 40.8 1.0 O D:GLN644 2.4 52.4 1.0 OD2 D:ASP623 2.5 47.4 1.0 OD2 D:ASP734 2.6 48.4 1.0 OD1 D:ASP734 2.7 46.2 1.0 CG D:ASP734 3.0 48.8 1.0 CG D:ASP623 3.4 48.7 1.0 C D:SER646 3.5 49.5 1.0 C D:ASN621 3.5 41.1 1.0 C D:GLN644 3.6 49.6 1.0 N D:SER646 3.7 46.8 1.0 OD1 D:ASP623 3.9 51.1 1.0 CA D:SER646 4.2 46.8 1.0 C D:GLY645 4.2 48.5 1.0 CB D:ASN621 4.2 45.8 1.0 O D:HOH909 4.2 47.0 1.0 CA D:ASN621 4.2 41.5 1.0 OD1 D:ASN735 4.2 48.8 1.0 N D:GLN644 4.4 54.0 1.0 CA D:GLY642 4.5 48.4 1.0 CA D:GLY645 4.5 52.4 1.0 CB D:ASP734 4.5 43.1 1.0 N D:GLY645 4.5 48.2 1.0 N D:ALA647 4.5 49.7 1.0 CA D:GLN644 4.5 49.9 1.0 N D:PHE622 4.6 41.6 1.0 CB D:ASP623 4.6 41.9 1.0 CB D:PHE622 4.6 41.5 1.0 C D:PHE622 4.7 43.0 1.0 N D:ASP623 4.7 43.5 1.0 N D:LEU643 4.8 50.8 1.0 CA D:PHE622 4.8 40.4 1.0 O D:GLY645 4.8 48.1 1.0 CA D:ALA647 4.9 44.3 1.0 CB D:SER646 4.9 46.0 1.0 CB D:GLN644 4.9 49.2 1.0

D.L.Abeyawardhane, S.E.Sevdalis, K.A.Adipietro, R.Godoy-Ruiz, K.M.Varney, I.F.Nawaz, A.X.Spittel, D.Hunter, R.R.Rustandi, V.I.Silin, A.Des Georges, M.E.Cook, E.Pozharski, D.J.Weber. Pore Formation By the Cdtb Component of the Clostridioides Difficile Binary Toxin Is Ca 2+ -Dependent. Commun Biol V. 8 901 2025.
ISSN: ESSN 2399-3642
PubMed: 40490540
DOI: 10.1038/S42003-025-08343-X