Calcium in PDB 9jsg: Clostridium Perfringens Iota Toxin Pore Ib in Pore State

The binding sites of Calcium atom in the Clostridium Perfringens Iota Toxin Pore Ib in Pore State (pdb code 9jsg). 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 Pore State, PDB code: 9jsg:
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 Pore 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 Pore State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:26.8 occ:1.00 O A:GLU262 2.5 28.1 1.0 O A:SER259 2.5 29.0 1.0 OE1 A:GLU230 2.5 30.7 1.0 OD2 A:ASP221 2.6 31.0 1.0 OD2 A:ASP272 2.6 25.1 1.0 OD2 A:ASP223 2.7 31.0 1.0 OE2 A:GLU230 2.9 30.7 1.0 CD A:GLU230 3.1 30.7 1.0 CG A:ASP223 3.1 31.0 1.0 C A:GLU262 3.6 28.1 1.0 OD1 A:ASP223 3.7 31.0 1.0 C A:SER259 3.7 29.0 1.0 CG A:ASP221 3.7 31.0 1.0 CG A:ASP272 3.7 25.1 1.0 CB A:ASP223 3.9 31.0 1.0 CA A:SER263 4.1 24.4 1.0 CB A:ASP272 4.2 25.1 1.0 N A:SER263 4.3 24.4 1.0 OD1 A:ASP221 4.3 31.0 1.0 CA A:TYR260 4.3 30.8 1.0 O A:SER263 4.4 24.4 1.0 C A:SER263 4.4 24.4 1.0 N A:TYR260 4.5 30.8 1.0 OG1 A:THR265 4.5 23.5 1.0 N A:GLU262 4.5 28.1 1.0 CG A:GLU230 4.6 30.7 1.0 CA A:CA902 4.6 35.0 1.0 OG A:SER258 4.6 29.1 1.0 N A:SER259 4.6 29.0 1.0 CB A:SER258 4.7 29.1 1.0 C A:TYR260 4.7 30.8 1.0 CA A:GLU262 4.7 28.1 1.0 CA A:SER259 4.7 29.0 1.0 OD1 A:ASP272 4.8 25.1 1.0 CB A:ASP221 4.9 31.0 1.0

Calcium binding site 2 out of 3 in the Clostridium Perfringens Iota Toxin Pore Ib in Pore 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 Pore State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:35.0 occ:1.00 OD1 A:ASP221 2.5 31.0 1.0 OE2 A:GLU230 2.5 30.7 1.0 O A:ILE225 2.5 30.8 1.0 OD1 A:ASP219 2.5 34.1 1.0 OD1 A:ASP223 2.7 31.0 1.0 OD1 A:ASP227 2.9 33.5 1.0 CG A:ASP221 3.4 31.0 1.0 CD A:GLU230 3.6 30.7 1.0 C A:ILE225 3.7 30.8 1.0 OD2 A:ASP221 3.7 31.0 1.0 CG A:ASP219 3.7 34.1 1.0 CG A:ASP223 3.8 31.0 1.0 O A:TYR260 3.8 30.8 1.0 N A:ASP227 3.9 33.5 1.0 C A:PRO226 3.9 33.5 1.0 CG A:ASP227 4.0 33.5 1.0 CA A:ASP219 4.1 34.1 1.0 N A:THR220 4.2 32.7 1.0 CA A:TYR260 4.2 30.8 1.0 CA A:ASP227 4.2 33.5 1.0 O A:PRO226 4.2 33.5 1.0 CG A:GLU230 4.2 30.7 1.0 CB A:TYR260 4.3 30.8 1.0 OD2 A:ASP223 4.4 31.0 1.0 N A:ASP221 4.4 31.0 1.0 CA A:PRO226 4.4 33.5 1.0 C A:TYR260 4.4 30.8 1.0 C A:ASP219 4.5 34.1 1.0 N A:PRO226 4.5 33.5 1.0 CB A:ASP219 4.5 34.1 1.0 CA A:CA901 4.6 26.8 1.0 OD2 A:ASP219 4.6 34.1 1.0 OE1 A:GLU230 4.6 30.7 1.0 CA A:ILE225 4.7 30.8 1.0 N A:ILE225 4.7 30.8 1.0 CB A:ASP227 4.7 33.5 1.0 CB A:ASP221 4.8 31.0 1.0 O A:LEU218 4.8 40.0 1.0 N A:ASP223 4.9 31.0 1.0 CB A:ILE225 4.9 30.8 1.0 CB A:ASP223 4.9 31.0 1.0 OD2 A:ASP227 5.0 33.5 1.0

Calcium binding site 3 out of 3 in the Clostridium Perfringens Iota Toxin Pore Ib in Pore 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 Pore State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:119.4 occ:1.00 O A:ASN620 2.6 120.1 1.0 O A:VAL645 2.6 128.3 1.0 OD2 A:ASP733 2.7 120.2 1.0 OD2 A:ASP622 2.9 124.4 1.0 OD1 A:ASP733 3.0 120.2 1.0 OD1 A:ASP622 3.2 124.4 1.0 CG A:ASP733 3.2 120.2 1.0 CG A:ASP622 3.4 124.4 1.0 N A:VAL645 3.6 128.3 1.0 N A:SER644 3.7 127.9 1.0 C A:ASN620 3.7 120.1 1.0 C A:VAL645 3.7 128.3 1.0 OE1 A:GLN643 3.9 124.6 1.0 N A:GLN643 3.9 124.6 1.0 CB A:ASN620 4.0 120.1 1.0 CA A:ASN620 4.2 120.1 1.0 OD1 A:ASN734 4.2 115.5 1.0 CA A:VAL645 4.3 128.3 1.0 CB A:GLN643 4.3 124.6 1.0 N A:LEU642 4.4 123.0 1.0 C A:SER644 4.4 127.9 1.0 CA A:GLN643 4.5 124.6 1.0 CA A:SER644 4.5 127.9 1.0 C A:GLN643 4.6 124.6 1.0 CG2 A:VAL645 4.7 128.3 1.0 CB A:ASP733 4.7 120.2 1.0 CB A:SER644 4.8 127.9 1.0 CA A:GLY641 4.8 128.6 1.0 CG A:ASN620 4.8 120.1 1.0 CB A:ASP622 4.8 124.4 1.0 N A:PHE621 4.8 122.4 1.0 N A:ALA646 4.9 129.7 1.0 CD A:GLN643 4.9 124.6 1.0 C A:GLY641 5.0 128.6 1.0 C A:LEU642 5.0 123.0 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.