Calcium in PDB 6uwr: Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Calcium atom in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation (pdb code 6uwr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 42 binding sites of Calcium where determined in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation, PDB code: 6uwr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:12.9 occ:1.00 OD2 A:ASP222 2.2 18.3 1.0 OD2 A:ASP273 2.3 14.8 1.0 O A:GLU263 2.3 17.3 1.0 O A:ASN260 2.3 15.2 1.0 OD2 A:ASP224 2.7 18.9 1.0 OE1 A:GLU231 2.7 16.8 1.0 OE2 A:GLU231 2.8 16.8 1.0 CD A:GLU231 3.1 16.8 1.0 CG A:ASP273 3.4 14.8 1.0 CG A:ASP222 3.5 18.3 1.0 C A:ASN260 3.5 15.2 1.0 C A:GLU263 3.5 17.3 1.0 CG A:ASP224 3.6 18.9 1.0 OD1 A:ASP224 3.9 18.9 1.0 CB A:ASP273 3.9 14.8 1.0 OG1 A:THR266 4.1 13.1 1.0 CA A:SER264 4.1 14.8 1.0 OD1 A:ASP222 4.2 18.3 1.0 CA A:TYR261 4.3 18.4 1.0 N A:SER264 4.3 14.8 1.0 N A:TYR261 4.3 18.4 1.0 O A:SER264 4.4 14.8 1.0 N A:ASN260 4.4 15.2 1.0 C A:SER264 4.4 14.8 1.0 CA A:CA902 4.4 14.5 1.0 CB A:ASP222 4.4 18.3 1.0 N A:GLU263 4.5 17.3 1.0 OD1 A:ASP273 4.5 14.8 1.0 CA A:ASN260 4.5 15.2 1.0 OG A:SER259 4.5 14.9 1.0 CA A:GLU263 4.6 17.3 1.0 CG A:GLU231 4.6 16.8 1.0 CB A:SER259 4.6 14.9 1.0 C A:TYR261 4.7 18.4 1.0 CB A:ASN260 5.0 15.2 1.0 CB A:ASP224 5.0 18.9 1.0

Calcium binding site 2 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:14.5 occ:1.00 OD1 A:ASP222 2.2 18.3 1.0 O A:ILE226 2.3 18.1 1.0 OD1 A:ASP224 2.3 18.9 1.0 OD1 A:ASP220 2.4 22.7 1.0 OE2 A:GLU231 2.5 16.8 1.0 CG A:ASP222 3.1 18.3 1.0 OD2 A:ASP222 3.2 18.3 1.0 C A:ILE226 3.5 18.1 1.0 CG A:ASP224 3.5 18.9 1.0 CG A:ASP220 3.6 22.7 1.0 CD A:GLU231 3.7 16.8 1.0 OD2 A:ASP224 4.0 18.9 1.0 OD1 A:ASP228 4.1 20.1 1.0 CG A:GLU231 4.2 16.8 1.0 O A:ASP224 4.2 18.9 1.0 OD2 A:ASP220 4.2 22.7 1.0 N A:ILE226 4.2 18.1 1.0 CA A:ILE226 4.2 18.1 1.0 C A:PRO227 4.3 19.5 1.0 CB A:ILE226 4.4 18.1 1.0 N A:ASP224 4.4 18.9 1.0 O A:PRO227 4.4 19.5 1.0 CA A:CA901 4.4 12.9 1.0 N A:PRO227 4.4 19.5 1.0 CB A:ASP222 4.5 18.3 1.0 N A:ASN223 4.5 21.2 1.0 O A:TYR261 4.5 18.4 1.0 CA A:PRO227 4.5 19.5 1.0 CA A:ASP220 4.5 22.7 1.0 N A:ASP222 4.6 18.3 1.0 C A:ASP224 4.6 18.9 1.0 N A:ASP228 4.6 20.1 1.0 CB A:ASP220 4.7 22.7 1.0 CB A:ASP224 4.7 18.9 1.0 OE1 A:GLU231 4.7 16.8 1.0 N A:THR221 4.7 21.9 1.0 CA A:ASP224 4.8 18.9 1.0 CA A:TYR261 4.8 18.4 1.0 CA A:ASP222 4.9 18.3 1.0 C A:ASP222 5.0 18.3 1.0 C A:ASP220 5.0 22.7 1.0

Calcium binding site 3 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:46.9 occ:1.00 OG A:SER646 2.2 58.4 1.0 OD2 A:ASP734 2.3 48.9 1.0 O A:GLN644 2.4 53.9 1.0 OD1 A:ASP734 2.5 48.9 1.0 O A:ASN621 2.6 50.9 1.0 CG A:ASP734 2.7 48.9 1.0 C A:GLN644 3.4 53.9 1.0 OD2 A:ASP623 3.5 56.1 1.0 OD1 A:ASP623 3.5 56.1 1.0 CB A:ASN621 3.6 50.9 1.0 CB A:SER646 3.6 58.4 1.0 C A:ASN621 3.6 50.9 1.0 N A:GLN644 3.8 53.9 1.0 CG A:ASP623 3.8 56.1 1.0 ND2 A:ASN735 3.8 45.0 1.0 CA A:ASN621 3.9 50.9 1.0 CA A:GLN644 3.9 53.9 1.0 CB A:GLN644 4.0 53.9 1.0 CB A:ASP734 4.2 48.9 1.0 OE1 A:GLN644 4.4 53.9 1.0 N A:SER646 4.4 58.4 1.0 N A:GLY645 4.5 57.2 1.0 CA A:SER646 4.6 58.4 1.0 CG A:ASN735 4.6 45.0 1.0 C A:GLY645 4.6 57.2 1.0 CG A:ASN621 4.7 50.9 1.0 OD1 A:ASN735 4.8 45.0 1.0 N A:PHE622 4.8 54.0 1.0 N A:ASN735 4.9 45.0 1.0 CD A:GLN644 4.9 53.9 1.0 N A:LEU643 5.0 52.9 1.0 C A:LEU643 5.0 52.9 1.0

Calcium binding site 4 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:13.2 occ:1.00 OD2 B:ASP222 2.3 17.8 1.0 O B:ASN260 2.3 15.3 1.0 OD2 B:ASP273 2.3 13.6 1.0 O B:GLU263 2.3 16.3 1.0 OE1 B:GLU231 2.7 16.6 1.0 OD2 B:ASP224 2.7 18.4 1.0 OE2 B:GLU231 2.8 16.6 1.0 CD B:GLU231 3.1 16.6 1.0 CG B:ASP273 3.4 13.6 1.0 C B:ASN260 3.5 15.3 1.0 CG B:ASP222 3.5 17.8 1.0 C B:GLU263 3.5 16.3 1.0 CG B:ASP224 3.7 18.4 1.0 OD1 B:ASP224 3.9 18.4 1.0 CB B:ASP273 3.9 13.6 1.0 OG1 B:THR266 4.1 11.6 1.0 CA B:SER264 4.2 13.3 1.0 CA B:TYR261 4.2 17.9 1.0 OD1 B:ASP222 4.3 17.8 1.0 N B:TYR261 4.3 17.9 1.0 N B:SER264 4.3 13.3 1.0 N B:ASN260 4.3 15.3 1.0 CA B:CA902 4.4 14.9 1.0 O B:SER264 4.4 13.3 1.0 N B:GLU263 4.4 16.3 1.0 CB B:ASP222 4.4 17.8 1.0 CA B:ASN260 4.4 15.3 1.0 C B:SER264 4.4 13.3 1.0 OD1 B:ASP273 4.5 13.6 1.0 OG B:SER259 4.5 14.7 1.0 CA B:GLU263 4.6 16.3 1.0 CG B:GLU231 4.6 16.6 1.0 CB B:SER259 4.6 14.7 1.0 C B:TYR261 4.7 17.9 1.0 CB B:ASN260 4.9 15.3 1.0

Calcium binding site 5 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:14.9 occ:1.00 OD1 B:ASP222 2.2 17.8 1.0 O B:ILE226 2.3 18.0 1.0 OD1 B:ASP224 2.4 18.4 1.0 OE2 B:GLU231 2.5 16.6 1.0 OD1 B:ASP220 2.5 22.6 1.0 CG B:ASP222 3.1 17.8 1.0 OD2 B:ASP222 3.2 17.8 1.0 C B:ILE226 3.5 18.0 1.0 CG B:ASP224 3.5 18.4 1.0 CD B:GLU231 3.6 16.6 1.0 CG B:ASP220 3.6 22.6 1.0 OD1 B:ASP228 4.0 20.8 1.0 OD2 B:ASP224 4.0 18.4 1.0 CG B:GLU231 4.1 16.6 1.0 O B:ASP224 4.3 18.4 1.0 CA B:ILE226 4.3 18.0 1.0 OD2 B:ASP220 4.3 22.6 1.0 N B:ILE226 4.3 18.0 1.0 C B:PRO227 4.3 19.6 1.0 CB B:ILE226 4.4 18.0 1.0 O B:PRO227 4.4 19.6 1.0 CA B:CA901 4.4 13.2 1.0 N B:ASP224 4.4 18.4 1.0 N B:PRO227 4.4 19.6 1.0 O B:TYR261 4.5 17.9 1.0 CB B:ASP222 4.5 17.8 1.0 CA B:PRO227 4.5 19.6 1.0 CA B:ASP220 4.6 22.6 1.0 N B:ASN223 4.6 21.1 1.0 N B:ASP222 4.6 17.8 1.0 N B:ASP228 4.6 20.8 1.0 C B:ASP224 4.6 18.4 1.0 OE1 B:GLU231 4.6 16.6 1.0 CB B:ASP220 4.7 22.6 1.0 CB B:ASP224 4.7 18.4 1.0 CA B:TYR261 4.7 17.9 1.0 N B:THR221 4.8 21.4 1.0 CA B:ASP224 4.8 18.4 1.0 CA B:ASP222 4.9 17.8 1.0 CA B:ASP228 5.0 20.8 1.0

Calcium binding site 6 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:46.1 occ:1.00 OG B:SER646 2.2 56.9 1.0 OD2 B:ASP734 2.3 48.1 1.0 O B:GLN644 2.4 52.1 1.0 OD1 B:ASP734 2.5 48.1 1.0 O B:ASN621 2.7 47.8 1.0 CG B:ASP734 2.7 48.1 1.0 C B:GLN644 3.4 52.1 1.0 OD2 B:ASP623 3.5 52.5 1.0 OD1 B:ASP623 3.5 52.5 1.0 CB B:SER646 3.6 56.9 1.0 CB B:ASN621 3.6 47.8 1.0 C B:ASN621 3.6 47.8 1.0 N B:GLN644 3.8 52.1 1.0 CG B:ASP623 3.8 52.5 1.0 ND2 B:ASN735 3.8 43.9 1.0 CA B:ASN621 3.9 47.8 1.0 CA B:GLN644 3.9 52.1 1.0 CB B:GLN644 4.0 52.1 1.0 CB B:ASP734 4.2 48.1 1.0 OE1 B:GLN644 4.4 52.1 1.0 N B:SER646 4.4 56.9 1.0 N B:GLY645 4.5 56.4 1.0 CA B:SER646 4.6 56.9 1.0 CG B:ASN735 4.6 43.9 1.0 C B:GLY645 4.6 56.4 1.0 CG B:ASN621 4.8 47.8 1.0 OD1 B:ASN735 4.8 43.9 1.0 N B:PHE622 4.9 51.3 1.0 CD B:GLN644 4.9 52.1 1.0 N B:ASN735 4.9 43.9 1.0 N B:LEU643 4.9 51.0 1.0 C B:LEU643 5.0 51.0 1.0

Calcium binding site 7 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:12.4 occ:1.00 O C:ASN260 2.2 14.8 1.0 OD2 C:ASP222 2.3 18.1 1.0 OD2 C:ASP273 2.3 14.7 1.0 O C:GLU263 2.4 17.2 1.0 OE1 C:GLU231 2.7 16.6 1.0 OE2 C:GLU231 2.7 16.6 1.0 OD2 C:ASP224 2.8 18.3 1.0 CD C:GLU231 3.1 16.6 1.0 C C:ASN260 3.4 14.8 1.0 CG C:ASP273 3.5 14.7 1.0 CG C:ASP222 3.5 18.1 1.0 C C:GLU263 3.6 17.2 1.0 CG C:ASP224 3.7 18.3 1.0 CB C:ASP273 4.0 14.7 1.0 OD1 C:ASP224 4.0 18.3 1.0 OG1 C:THR266 4.0 13.1 1.0 CA C:TYR261 4.2 17.7 1.0 CA C:SER264 4.2 14.7 1.0 N C:TYR261 4.2 17.7 1.0 OD1 C:ASP222 4.3 18.1 1.0 N C:ASN260 4.3 14.8 1.0 N C:SER264 4.4 14.7 1.0 CA C:ASN260 4.4 14.8 1.0 CA C:CA902 4.4 15.4 1.0 N C:GLU263 4.4 17.2 1.0 CB C:ASP222 4.5 18.1 1.0 OG C:SER259 4.5 14.8 1.0 O C:SER264 4.5 14.7 1.0 C C:SER264 4.5 14.7 1.0 OD1 C:ASP273 4.5 14.7 1.0 CG C:GLU231 4.5 16.6 1.0 CB C:SER259 4.6 14.8 1.0 CA C:GLU263 4.6 17.2 1.0 C C:TYR261 4.6 17.7 1.0 CB C:ASN260 4.9 14.8 1.0 C C:SER259 5.0 14.8 1.0

Calcium binding site 8 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca902 b:15.4 occ:1.00 OD1 C:ASP222 2.2 18.1 1.0 O C:ILE226 2.3 17.9 1.0 OD1 C:ASP224 2.4 18.3 1.0 OE2 C:GLU231 2.4 16.6 1.0 OD1 C:ASP220 2.5 22.4 1.0 CG C:ASP222 3.1 18.1 1.0 OD2 C:ASP222 3.2 18.1 1.0 C C:ILE226 3.5 17.9 1.0 CG C:ASP224 3.5 18.3 1.0 CD C:GLU231 3.6 16.6 1.0 CG C:ASP220 3.7 22.4 1.0 OD1 C:ASP228 4.0 20.3 1.0 OD2 C:ASP224 4.1 18.3 1.0 CG C:GLU231 4.1 16.6 1.0 C C:PRO227 4.3 19.5 1.0 CA C:ILE226 4.3 17.9 1.0 N C:ILE226 4.3 17.9 1.0 OD2 C:ASP220 4.3 22.4 1.0 O C:ASP224 4.3 18.3 1.0 O C:PRO227 4.3 19.5 1.0 CB C:ILE226 4.4 17.9 1.0 CA C:CA901 4.4 12.4 1.0 N C:PRO227 4.4 19.5 1.0 O C:TYR261 4.5 17.7 1.0 N C:ASP224 4.5 18.3 1.0 CB C:ASP222 4.5 18.1 1.0 CA C:PRO227 4.5 19.5 1.0 CA C:ASP220 4.6 22.4 1.0 N C:ASP228 4.6 20.3 1.0 N C:ASP222 4.6 18.1 1.0 N C:ASN223 4.6 21.2 1.0 OE1 C:GLU231 4.6 16.6 1.0 C C:ASP224 4.7 18.3 1.0 CA C:TYR261 4.7 17.7 1.0 CB C:ASP220 4.7 22.4 1.0 CB C:ASP224 4.7 18.3 1.0 N C:THR221 4.8 21.5 1.0 CA C:ASP224 4.9 18.3 1.0 CA C:ASP228 4.9 20.3 1.0 CA C:ASP222 4.9 18.1 1.0 C C:TYR261 5.0 17.7 1.0 CB C:TYR261 5.0 17.7 1.0

Calcium binding site 9 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca903 b:46.0 occ:1.00 OG C:SER646 2.2 56.6 1.0 OD2 C:ASP734 2.3 48.4 1.0 O C:GLN644 2.4 52.5 1.0 OD1 C:ASP734 2.5 48.4 1.0 O C:ASN621 2.7 49.5 1.0 CG C:ASP734 2.7 48.4 1.0 C C:GLN644 3.4 52.5 1.0 OD2 C:ASP623 3.5 54.0 1.0 OD1 C:ASP623 3.5 54.0 1.0 CB C:SER646 3.6 56.6 1.0 CB C:ASN621 3.6 49.5 1.0 C C:ASN621 3.6 49.5 1.0 N C:GLN644 3.7 52.5 1.0 CG C:ASP623 3.8 54.0 1.0 ND2 C:ASN735 3.8 44.6 1.0 CA C:GLN644 3.9 52.5 1.0 CA C:ASN621 3.9 49.5 1.0 CB C:GLN644 4.0 52.5 1.0 CB C:ASP734 4.2 48.4 1.0 OE1 C:GLN644 4.4 52.5 1.0 N C:SER646 4.4 56.6 1.0 N C:GLY645 4.4 55.8 1.0 CA C:SER646 4.6 56.6 1.0 C C:GLY645 4.6 55.8 1.0 CG C:ASN735 4.6 44.6 1.0 CG C:ASN621 4.8 49.5 1.0 OD1 C:ASN735 4.8 44.6 1.0 N C:PHE622 4.9 52.0 1.0 CD C:GLN644 4.9 52.5 1.0 N C:ASN735 4.9 44.6 1.0 N C:LEU643 4.9 51.2 1.0 C C:LEU643 4.9 51.2 1.0 CA C:GLY645 5.0 55.8 1.0

Calcium binding site 10 out of 42 in the Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Clostridium Difficile Binary Toxin Translocase Cdtb in Asymmetric Tetradecamer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca901 b:12.6 occ:1.00 O D:ASN260 2.3 15.1 1.0 OD2 D:ASP222 2.3 17.9 1.0 OD2 D:ASP273 2.3 14.9 1.0 O D:GLU263 2.4 17.1 1.0 OE1 D:GLU231 2.6 15.9 1.0 OE2 D:GLU231 2.7 15.9 1.0 OD2 D:ASP224 2.8 18.6 1.0 CD D:GLU231 3.0 15.9 1.0 C D:ASN260 3.4 15.1 1.0 CG D:ASP273 3.4 14.9 1.0 CG D:ASP222 3.5 17.9 1.0 C D:GLU263 3.6 17.1 1.0 CG D:ASP224 3.7 18.6 1.0 CB D:ASP273 3.9 14.9 1.0 OD1 D:ASP224 4.0 18.6 1.0 OG1 D:THR266 4.0 13.2 1.0 CA D:TYR261 4.2 17.7 1.0 N D:TYR261 4.2 17.7 1.0 CA D:SER264 4.3 15.0 1.0 N D:ASN260 4.3 15.1 1.0 OD1 D:ASP222 4.3 17.9 1.0 CA D:CA902 4.4 14.3 1.0 N D:SER264 4.4 15.0 1.0 CA D:ASN260 4.4 15.1 1.0 OG D:SER259 4.4 14.5 1.0 O D:SER264 4.5 15.0 1.0 N D:GLU263 4.5 17.1 1.0 OD1 D:ASP273 4.5 14.9 1.0 CB D:ASP222 4.5 17.9 1.0 C D:SER264 4.5 15.0 1.0 CG D:GLU231 4.5 15.9 1.0 CB D:SER259 4.5 14.5 1.0 CA D:GLU263 4.6 17.1 1.0 C D:TYR261 4.7 17.7 1.0 CB D:ASN260 4.9 15.1 1.0 C D:SER259 5.0 14.5 1.0

X.Xu, R.Godoy-Ruiz, K.A.Adipietro, C.Peralta, D.Ben-Hail, K.M.Varney, M.E.Cook, B.M.Roth, P.T.Wilder, T.Cleveland, A.Grishaev, H.M.Neu, S.L.J.Michel, W.Yu, D.Beckett, R.R.Rustandi, C.Lancaster, J.W.Loughney, A.Kristopeit, S.Christanti, J.W.Olson, A.D.Mackerell, A.D.Georges, E.Pozharski, D.J.Weber. Structure of the Cell-Binding Component of Theclostridium Difficilebinary Toxin Reveals A Di-Heptamer Macromolecular Assembly. Proc.Natl.Acad.Sci.Usa V. 117 1049 2020.
ISSN: ESSN 1091-6490
PubMed: 31896582
DOI: 10.1073/PNAS.1919490117