Calcium in PDB 9jso: Clostridium Perfringens Iota Toxin Pore Ib in Prepore VIII State

The binding sites of Calcium atom in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VIII State (pdb code 9jso). 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 VIII State, PDB code: 9jso:
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 VIII 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 VIII State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:15.9 occ:1.00 O A:SER259 2.5 18.1 1.0 OD2 A:ASP221 2.5 23.1 1.0 O A:GLU262 2.5 20.4 1.0 OD2 A:ASP272 2.6 12.3 1.0 OD2 A:ASP223 2.6 23.0 1.0 OE2 A:GLU230 2.6 16.5 1.0 OE1 A:GLU230 2.8 16.5 1.0 CD A:GLU230 3.1 16.5 1.0 C A:GLU262 3.6 20.4 1.0 CG A:ASP223 3.6 23.0 1.0 CG A:ASP221 3.6 23.1 1.0 CG A:ASP272 3.7 12.3 1.0 C A:SER259 3.7 18.1 1.0 OD1 A:ASP223 4.0 23.0 1.0 CA A:SER263 4.1 13.8 1.0 CB A:ASP272 4.1 12.3 1.0 OD1 A:ASP221 4.2 23.1 1.0 N A:SER263 4.2 13.8 1.0 CA A:TYR260 4.3 22.1 1.0 OG1 A:THR265 4.4 14.3 1.0 CA A:CA902 4.4 10.5 1.0 O A:SER263 4.4 13.8 1.0 OG A:SER258 4.4 14.7 1.0 N A:TYR260 4.5 22.1 1.0 N A:GLU262 4.5 20.4 1.0 C A:SER263 4.5 13.8 1.0 CG A:GLU230 4.6 16.5 1.0 CA A:GLU262 4.7 20.4 1.0 CB A:SER258 4.7 14.7 1.0 N A:SER259 4.7 18.1 1.0 C A:TYR260 4.7 22.1 1.0 OD1 A:ASP272 4.7 12.3 1.0 CB A:ASP223 4.7 23.0 1.0 CA A:SER259 4.7 18.1 1.0 CB A:ASP221 4.8 23.1 1.0

Calcium binding site 2 out of 3 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VIII 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 VIII State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:10.5 occ:1.00 OD1 A:ASP221 2.4 23.1 1.0 OE2 A:GLU230 2.5 16.5 1.0 OD1 A:ASP219 2.5 23.6 1.0 O A:ILE225 2.5 17.0 1.0 OD1 A:ASP223 2.8 23.0 1.0 OD1 A:ASP227 3.2 25.9 1.0 CG A:ASP221 3.3 23.1 1.0 CD A:GLU230 3.5 16.5 1.0 OD2 A:ASP221 3.6 23.1 1.0 C A:ILE225 3.7 17.0 1.0 CG A:ASP219 3.7 23.6 1.0 CG A:ASP223 3.8 23.0 1.0 CG A:GLU230 4.0 16.5 1.0 O A:TYR260 4.1 22.1 1.0 OD2 A:ASP223 4.2 23.0 1.0 C A:PRO226 4.2 17.0 1.0 N A:ASP227 4.3 25.9 1.0 CA A:ASP219 4.3 23.6 1.0 CA A:TYR260 4.4 22.1 1.0 CG A:ASP227 4.4 25.9 1.0 CA A:CA901 4.4 15.9 1.0 O A:PRO226 4.4 17.0 1.0 N A:ASP221 4.4 23.1 1.0 N A:THR220 4.4 21.5 1.0 OD2 A:ASP219 4.4 23.6 1.0 CA A:ILE225 4.5 17.0 1.0 CB A:ILE225 4.5 17.0 1.0 CA A:ASP227 4.5 25.9 1.0 N A:ILE225 4.5 17.0 1.0 CB A:TYR260 4.6 22.1 1.0 CB A:ASP219 4.6 23.6 1.0 N A:PRO226 4.6 17.0 1.0 OE1 A:GLU230 4.6 16.5 1.0 C A:TYR260 4.6 22.1 1.0 CB A:ASP221 4.7 23.1 1.0 CA A:PRO226 4.7 17.0 1.0 C A:ASP219 4.7 23.6 1.0 N A:ASP223 4.8 23.0 1.0 N A:ASN222 4.8 27.2 1.0 CA A:ASP221 5.0 23.1 1.0 CB A:GLU230 5.0 16.5 1.0

Calcium binding site 3 out of 3 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VIII 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 VIII State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:123.3 occ:1.00 OD2 A:ASP733 2.6 120.9 1.0 O A:VAL645 2.6 134.8 1.0 OD1 A:ASP733 2.6 120.9 1.0 OD2 A:ASP622 2.9 129.6 1.0 O A:ASN620 2.9 121.8 1.0 CG A:ASP733 2.9 120.9 1.0 NE2 A:GLN643 3.1 129.6 1.0 CD A:GLN643 3.6 129.6 1.0 CG A:ASP622 3.8 129.6 1.0 CG A:GLN643 3.8 129.6 1.0 C A:VAL645 3.8 134.8 1.0 C A:ASN620 4.1 121.8 1.0 N A:VAL645 4.2 134.8 1.0 CB A:ASN620 4.3 121.8 1.0 OD1 A:ASP622 4.3 129.6 1.0 OE1 A:GLN643 4.4 129.6 1.0 CB A:ASP733 4.5 120.9 1.0 CA A:ASN620 4.5 121.8 1.0 N A:SER644 4.6 135.3 1.0 N A:GLN643 4.6 129.6 1.0 N A:LEU642 4.6 126.1 1.0 CA A:VAL645 4.6 134.8 1.0 N A:ALA646 4.8 134.9 1.0 CB A:ASP622 4.8 129.6 1.0 ND2 A:ASN620 4.8 121.8 1.0 OD1 A:ASN734 4.8 113.5 1.0 CA A:ALA646 4.9 134.9 1.0 CG2 A:VAL645 4.9 134.8 1.0 CG A:ASN620 4.9 121.8 1.0 CA A:GLY641 4.9 131.1 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.