Calcium in PDB 9jsf: Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State

The binding sites of Calcium atom in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State (pdb code 9jsf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State, PDB code: 9jsf:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:9.4 occ:1.00 OE2 A:GLU230 2.2 1.2 1.0 O A:GLU262 2.3 4.7 1.0 OD2 A:ASP221 2.4 2.9 1.0 O A:SER259 2.4 2.5 1.0 OD2 A:ASP272 2.5 1.4 1.0 OD2 A:ASP223 3.0 1.4 1.0 CD A:GLU230 3.2 1.2 1.0 C A:GLU262 3.4 4.7 1.0 CG A:ASP272 3.6 1.4 1.0 CG A:ASP221 3.6 2.9 1.0 C A:SER259 3.7 2.5 1.0 OE1 A:GLU230 3.7 1.2 1.0 CG A:ASP223 3.8 1.4 1.0 CA A:SER263 3.8 3.3 1.0 N A:SER263 4.1 3.3 1.0 OD1 A:ASP223 4.1 1.4 1.0 O A:SER263 4.1 3.3 1.0 CB A:ASP272 4.1 1.4 1.0 OG1 A:THR265 4.2 9.4 1.0 C A:SER263 4.2 3.3 1.0 OD1 A:ASP221 4.3 2.9 1.0 CA A:CA802 4.4 9.4 1.0 CG A:GLU230 4.4 1.2 1.0 N A:GLU262 4.5 4.7 1.0 CA A:TYR260 4.5 1.0 1.0 N A:TYR260 4.5 1.0 1.0 CA A:GLU262 4.6 4.7 1.0 OD1 A:ASP272 4.6 1.4 1.0 N A:SER259 4.6 2.5 1.0 CB A:ASP221 4.6 2.9 1.0 OG A:SER258 4.6 1.1 1.0 CA A:SER259 4.7 2.5 1.0 C A:TYR260 4.8 1.0 1.0 CB A:ASP223 4.9 1.4 1.0 CB A:SER258 4.9 1.1 1.0

Calcium binding site 2 out of 3 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:9.4 occ:1.00 OD1 A:ASP221 2.3 2.9 1.0 O A:ILE225 2.3 0.8 1.0 OD1 A:ASP219 2.4 2.4 1.0 OD1 A:ASP223 2.4 1.4 1.0 OE1 A:GLU230 2.5 1.2 1.0 CG A:ASP221 3.2 2.9 1.0 OD2 A:ASP221 3.3 2.9 1.0 C A:ILE225 3.5 0.8 1.0 CG A:ASP223 3.5 1.4 1.0 CD A:GLU230 3.6 1.2 1.0 CG A:ASP219 3.6 2.4 1.0 OD2 A:ASP223 4.0 1.4 1.0 OE2 A:GLU230 4.0 1.2 1.0 CB A:ILE225 4.1 0.8 1.0 N A:ILE225 4.1 0.8 1.0 CA A:ILE225 4.1 0.8 1.0 OD1 A:ASP227 4.2 3.1 1.0 OD2 A:ASP219 4.3 2.4 1.0 CA A:CA801 4.4 9.4 1.0 N A:ASP223 4.5 1.4 1.0 C A:PRO226 4.5 1.8 1.0 CA A:ASP219 4.5 2.4 1.0 N A:PRO226 4.6 1.8 1.0 O A:PRO226 4.6 1.8 1.0 N A:ASP221 4.6 2.9 1.0 CB A:ASP221 4.6 2.9 1.0 O A:TYR260 4.6 1.0 1.0 CB A:ASP219 4.7 2.4 1.0 CA A:PRO226 4.8 1.8 1.0 CB A:ASP223 4.8 1.4 1.0 CA A:TYR260 4.8 1.0 1.0 N A:ASP227 4.8 3.1 1.0 N A:ASN222 4.8 2.4 1.0 N A:THR220 4.8 2.8 1.0 CG A:GLU230 4.8 1.2 1.0 CB A:GLU230 4.9 1.2 1.0 CG2 A:ILE225 4.9 0.8 1.0 C A:ASP219 4.9 2.4 1.0 C A:ASP223 5.0 1.4 1.0 CA A:ASP223 5.0 1.4 1.0

Calcium binding site 3 out of 3 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore I State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:13.0 occ:1.00 OD2 A:ASP733 2.5 14.3 1.0 OD1 A:ASP733 2.5 14.3 1.0 OD2 A:ASP622 2.5 19.0 1.0 O A:VAL645 2.6 16.7 1.0 O A:ASN620 2.6 15.3 1.0 CG A:ASP733 2.9 14.3 1.0 OD1 A:ASP622 3.0 19.0 1.0 CG A:ASP622 3.1 19.0 1.0 C A:ASN620 3.7 15.3 1.0 C A:VAL645 3.8 16.7 1.0 N A:VAL645 3.9 16.7 1.0 N A:SER644 4.1 17.9 1.0 CB A:ASN620 4.2 15.3 1.0 N A:GLN643 4.3 18.3 1.0 CA A:ASN620 4.3 15.3 1.0 CB A:ASP733 4.4 14.3 1.0 CB A:ASP622 4.5 19.0 1.0 N A:LEU642 4.5 16.4 1.0 CA A:VAL645 4.5 16.7 1.0 OE1 A:GLN643 4.5 18.3 1.0 ND2 A:ASN734 4.6 14.5 1.0 CB A:GLN643 4.8 18.3 1.0 N A:ASP622 4.8 19.0 1.0 N A:ALA646 4.8 16.2 1.0 N A:PHE621 4.8 15.6 1.0 C A:SER644 4.8 17.9 1.0 CA A:GLY641 4.9 15.3 1.0 CA A:SER644 4.9 17.9 1.0 CA A:GLN643 4.9 18.3 1.0 CB A:PHE621 4.9 15.6 1.0 C A:PHE621 4.9 15.6 1.0 CG A:ASN620 4.9 15.3 1.0 CA A:ALA646 5.0 16.2 1.0 CG2 A:VAL645 5.0 16.7 1.0

T.Yamada, Y.Sugita, T.Yoshida, T.Noda, H.Tsuge. Step-By-Step Maturation Mechanism of Binary Toxin Pore Revealed By Cryo-Em Analysis To Be Published.