Calcium in PDB 9jsm: Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Calcium atom in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State (pdb code 9jsm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 21 binding sites of Calcium where determined in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State, PDB code: 9jsm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI 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 VI State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:8.6 occ:1.00 OD2 A:ASP223 2.3 8.6 1.0 OD2 A:ASP272 2.3 0.5 1.0 O A:GLU262 2.4 2.7 1.0 OE2 A:GLU230 2.4 14.2 1.0 OD2 A:ASP221 2.5 5.3 1.0 O A:SER259 3.0 5.8 1.0 CG A:ASP223 3.4 8.6 1.0 CG A:ASP272 3.4 0.5 1.0 CD A:GLU230 3.5 14.2 1.0 C A:GLU262 3.5 2.7 1.0 CG A:ASP221 3.7 5.3 1.0 OE1 A:GLU230 3.9 14.2 1.0 CB A:ASP272 4.0 0.5 1.0 OD1 A:ASP223 4.1 8.6 1.0 C A:SER259 4.2 5.8 1.0 CA A:SER263 4.2 8.6 1.0 CB A:ASP223 4.2 8.6 1.0 N A:SER263 4.3 8.6 1.0 N A:GLU262 4.3 2.7 1.0 O A:SER263 4.3 8.6 1.0 OD1 A:ASP272 4.4 0.5 1.0 OG1 A:THR265 4.4 8.6 1.0 C A:SER263 4.5 8.6 1.0 CA A:TYR260 4.5 8.0 1.0 CA A:GLU262 4.5 2.7 1.0 OD1 A:ASP221 4.6 5.3 1.0 CB A:ASP221 4.6 5.3 1.0 CG A:GLU230 4.7 14.2 1.0 CA A:CA802 4.8 21.0 1.0 N A:TYR260 4.8 8.0 1.0 C A:TYR260 4.9 8.0 1.0

Calcium binding site 2 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI 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 VI State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:21.0 occ:1.00 OD1 A:ASP221 2.3 5.3 1.0 OE1 A:GLU230 2.4 14.2 1.0 O A:ILE225 2.4 9.1 1.0 OD1 A:ASP223 2.4 8.6 1.0 OD1 A:ASP219 2.5 13.2 1.0 OD1 A:ASP227 3.0 8.6 1.0 CG A:ASP221 3.2 5.3 1.0 OD2 A:ASP221 3.3 5.3 1.0 CG A:ASP223 3.4 8.6 1.0 CD A:GLU230 3.6 14.2 1.0 C A:ILE225 3.6 9.1 1.0 OD2 A:ASP223 3.7 8.6 1.0 CG A:ASP219 3.8 13.2 1.0 OE2 A:GLU230 4.1 14.2 1.0 CG A:ASP227 4.2 8.6 1.0 CA A:ILE225 4.3 9.1 1.0 CB A:ILE225 4.3 9.1 1.0 N A:ILE225 4.3 9.1 1.0 C A:PRO226 4.4 21.2 1.0 N A:ASP227 4.4 8.6 1.0 N A:ASP221 4.4 5.3 1.0 OD2 A:ASP219 4.5 13.2 1.0 CA A:ASP219 4.6 13.2 1.0 CB A:ASP221 4.6 5.3 1.0 N A:THR220 4.6 8.7 1.0 N A:PRO226 4.6 21.2 1.0 N A:ASP223 4.7 8.6 1.0 CA A:ASP227 4.7 8.6 1.0 O A:PRO226 4.7 21.2 1.0 O A:TYR260 4.7 8.0 1.0 CB A:GLU230 4.7 14.2 1.0 CA A:PRO226 4.7 21.2 1.0 CG A:GLU230 4.7 14.2 1.0 CB A:ASP223 4.8 8.6 1.0 CB A:ASP219 4.8 13.2 1.0 CB A:TYR260 4.8 8.0 1.0 CA A:CA801 4.8 8.6 1.0 CA A:TYR260 4.8 8.0 1.0 C A:ASP219 4.9 13.2 1.0 N A:ASN222 4.9 3.6 1.0 CA A:ASP221 5.0 5.3 1.0 OD2 A:ASP227 5.0 8.6 1.0

Calcium binding site 3 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI 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 VI State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:71.3 occ:1.00 N A:SER644 2.6 87.6 1.0 O A:VAL645 2.6 84.7 1.0 OD2 A:ASP733 2.7 85.4 1.0 N A:GLN643 2.8 85.2 1.0 N A:VAL645 2.9 84.7 1.0 CD A:GLN643 3.0 85.2 1.0 OE1 A:GLN643 3.1 85.2 1.0 OD2 A:ASP622 3.1 84.9 1.0 CG A:GLN643 3.2 85.2 1.0 C A:GLN643 3.4 85.2 1.0 N A:LEU642 3.4 86.7 1.0 CA A:GLN643 3.4 85.2 1.0 C A:SER644 3.5 87.6 1.0 C A:VAL645 3.5 84.7 1.0 CA A:SER644 3.5 87.6 1.0 NE2 A:GLN643 3.5 85.2 1.0 C A:GLY641 3.6 85.4 1.0 CA A:GLY641 3.6 85.4 1.0 CA A:VAL645 3.8 84.7 1.0 CG A:ASP733 3.8 85.4 1.0 CB A:GLN643 3.8 85.2 1.0 C A:LEU642 3.9 86.7 1.0 CA A:LEU642 4.1 86.7 1.0 OD1 A:ASP733 4.1 85.4 1.0 CG A:ASP622 4.2 84.9 1.0 CB A:SER644 4.2 87.6 1.0 O A:GLY641 4.3 85.4 1.0 O A:GLN643 4.5 85.2 1.0 O A:SER644 4.5 87.6 1.0 N A:GLY641 4.5 85.4 1.0 OD1 A:ASP622 4.6 84.9 1.0 N A:ALA646 4.7 93.1 1.0 CB A:LEU642 4.7 86.7 1.0 CG2 A:VAL645 4.9 84.7 1.0 O A:LEU642 5.0 86.7 1.0 CB A:VAL645 5.0 84.7 1.0

Calcium binding site 4 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:8.6 occ:1.00 OD2 B:ASP272 2.4 2.7 1.0 OD2 B:ASP223 2.4 8.9 1.0 O B:GLU262 2.4 8.2 1.0 OD2 B:ASP221 2.7 6.2 1.0 OE2 B:GLU230 2.7 8.0 1.0 O B:SER259 3.1 9.9 1.0 CG B:ASP272 3.3 2.7 1.0 CG B:ASP223 3.4 8.9 1.0 O B:SER263 3.5 8.2 1.0 CD B:GLU230 3.5 8.0 1.0 C B:GLU262 3.6 8.2 1.0 OE1 B:GLU230 3.7 8.0 1.0 CB B:ASP272 3.7 2.7 1.0 CG B:ASP221 3.8 6.2 1.0 OG1 B:THR265 3.9 8.6 1.0 C B:SER263 3.9 8.2 1.0 OD1 B:ASP223 4.0 8.9 1.0 CA B:SER263 4.0 8.2 1.0 OD1 B:ASP272 4.3 2.7 1.0 N B:SER263 4.3 8.2 1.0 CB B:ASP223 4.3 8.9 1.0 C B:SER259 4.3 9.9 1.0 CA B:CA802 4.4 8.6 1.0 CB B:ASP221 4.5 6.2 1.0 OD1 B:ASP221 4.8 6.2 1.0 N B:GLU262 4.8 8.2 1.0 CA B:GLU262 4.8 8.2 1.0 N B:ASN264 4.9 8.6 1.0 CA B:TYR260 4.9 12.2 1.0 OG B:SER258 4.9 6.3 1.0 CG B:GLU230 5.0 8.0 1.0 N B:THR265 5.0 8.6 1.0 CA B:ASP272 5.0 2.7 1.0

Calcium binding site 5 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:8.6 occ:1.00 OD1 B:ASP221 2.3 6.2 1.0 OD1 B:ASP223 2.4 8.9 1.0 OE1 B:GLU230 2.4 8.0 1.0 O B:ILE225 2.5 10.2 1.0 OD2 B:ASP221 2.6 6.2 1.0 CG B:ASP221 2.8 6.2 1.0 OD1 B:ASP219 2.9 11.5 1.0 CG B:ASP223 3.4 8.9 1.0 OD2 B:ASP223 3.6 8.9 1.0 C B:ILE225 3.6 10.2 1.0 CD B:GLU230 3.6 8.0 1.0 OD1 B:ASP227 3.8 9.1 1.0 CB B:ILE225 4.1 10.2 1.0 CG B:ASP219 4.1 11.5 1.0 CA B:ILE225 4.2 10.2 1.0 OE2 B:GLU230 4.3 8.0 1.0 CB B:ASP221 4.3 6.2 1.0 CA B:CA801 4.4 8.6 1.0 N B:ILE225 4.4 10.2 1.0 CA B:TYR260 4.4 12.2 1.0 O B:TYR260 4.4 12.2 1.0 CB B:TYR260 4.5 12.2 1.0 CB B:GLU230 4.6 8.0 1.0 C B:PRO226 4.6 25.2 1.0 CG2 B:ILE225 4.7 10.2 1.0 N B:ASP223 4.7 8.9 1.0 N B:PRO226 4.7 25.2 1.0 OD2 B:ASP219 4.7 11.5 1.0 N B:ASP221 4.7 6.2 1.0 CG B:GLU230 4.7 8.0 1.0 CB B:ASP223 4.7 8.9 1.0 N B:ASP227 4.8 9.1 1.0 O B:PRO226 4.8 25.2 1.0 C B:TYR260 4.8 12.2 1.0 CA B:PRO226 4.9 25.2 1.0 N B:ASN222 4.9 6.9 1.0 CG B:ASP227 4.9 9.1 1.0

Calcium binding site 6 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:81.8 occ:1.00 O B:VAL645 2.6 91.2 1.0 OD2 B:ASP622 2.6 93.8 1.0 N B:SER644 2.7 94.7 1.0 CD B:GLN643 2.7 93.1 1.0 OD2 B:ASP733 2.8 96.0 1.0 N B:GLN643 2.9 93.1 1.0 N B:VAL645 2.9 91.2 1.0 OE1 B:GLN643 2.9 93.1 1.0 CG B:GLN643 3.0 93.1 1.0 NE2 B:GLN643 3.2 93.1 1.0 C B:GLN643 3.4 93.1 1.0 CA B:GLN643 3.4 93.1 1.0 C B:VAL645 3.5 91.2 1.0 N B:LEU642 3.5 88.1 1.0 C B:SER644 3.5 94.7 1.0 CA B:SER644 3.6 94.7 1.0 CB B:GLN643 3.7 93.1 1.0 CG B:ASP622 3.8 93.8 1.0 C B:GLY641 3.8 92.1 1.0 CA B:VAL645 3.8 91.2 1.0 CG B:ASP733 3.8 96.0 1.0 CA B:GLY641 3.8 92.1 1.0 C B:LEU642 3.9 88.1 1.0 OD1 B:ASP733 4.1 96.0 1.0 CA B:LEU642 4.2 88.1 1.0 CB B:SER644 4.3 94.7 1.0 OD1 B:ASP622 4.4 93.8 1.0 O B:GLN643 4.6 93.1 1.0 O B:GLY641 4.6 92.1 1.0 O B:SER644 4.6 94.7 1.0 CB B:LEU642 4.6 88.1 1.0 N B:ALA646 4.7 93.6 1.0 CG2 B:VAL645 4.7 91.2 1.0 N B:GLY641 4.8 92.1 1.0 O B:ASN620 4.8 87.5 1.0 CB B:VAL645 4.9 91.2 1.0 CB B:ASP622 4.9 93.8 1.0

Calcium binding site 7 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:19.3 occ:1.00 OE2 C:GLU230 2.4 12.0 1.0 OD2 C:ASP223 2.4 12.5 1.0 OD2 C:ASP221 2.4 10.6 1.0 OD2 C:ASP272 2.5 9.4 1.0 O C:SER259 2.6 10.4 1.0 O C:GLU262 2.9 7.6 1.0 CD C:GLU230 3.1 12.0 1.0 OE1 C:GLU230 3.1 12.0 1.0 CG C:ASP223 3.4 12.5 1.0 CA C:CA802 3.5 16.4 1.0 CG C:ASP272 3.6 9.4 1.0 CG C:ASP221 3.7 10.6 1.0 C C:SER259 3.8 10.4 1.0 CB C:ASP272 3.9 9.4 1.0 OD1 C:ASP223 4.0 12.5 1.0 OG1 C:THR265 4.1 8.3 1.0 C C:GLU262 4.2 7.6 1.0 CA C:TYR260 4.4 15.2 1.0 OD1 C:ASP221 4.5 10.6 1.0 CG C:GLU230 4.5 12.0 1.0 CB C:ASP223 4.5 12.5 1.0 N C:TYR260 4.6 15.2 1.0 CB C:ASP221 4.6 10.6 1.0 O C:SER263 4.6 8.6 1.0 N C:GLU262 4.6 7.6 1.0 OD1 C:ASP272 4.7 9.4 1.0 C C:TYR260 4.7 15.2 1.0 N C:SER259 4.9 10.4 1.0 CA C:SER259 4.9 10.4 1.0 N C:LEU261 4.9 11.6 1.0 C C:SER263 5.0 8.6 1.0

Calcium binding site 8 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:16.4 occ:1.00 OD1 C:ASP223 2.4 12.5 1.0 OD1 C:ASP221 2.4 10.6 1.0 OE1 C:GLU230 2.5 12.0 1.0 OD2 C:ASP221 2.6 10.6 1.0 CG C:ASP221 2.9 10.6 1.0 O C:ILE225 3.0 13.1 1.0 OD1 C:ASP219 3.1 10.0 1.0 CG C:ASP223 3.1 12.5 1.0 OD2 C:ASP223 3.2 12.5 1.0 CA C:CA801 3.5 19.3 1.0 CD C:GLU230 3.6 12.0 1.0 CB C:ILE225 3.9 13.1 1.0 C C:ILE225 3.9 13.1 1.0 OE2 C:GLU230 4.1 12.0 1.0 CG C:ASP219 4.2 10.0 1.0 CA C:TYR260 4.2 15.2 1.0 CA C:ILE225 4.3 13.1 1.0 CG2 C:ILE225 4.3 13.1 1.0 O C:TYR260 4.3 15.2 1.0 CB C:ASP221 4.4 10.6 1.0 N C:ILE225 4.4 13.1 1.0 C C:TYR260 4.6 15.2 1.0 CB C:ASP223 4.6 12.5 1.0 OD2 C:ASP219 4.7 10.0 1.0 CB C:TYR260 4.7 15.2 1.0 O C:SER259 4.7 10.4 1.0 CG C:GLU230 4.8 12.0 1.0 N C:ASP223 4.8 12.5 1.0 CB C:GLU230 4.8 12.0 1.0 N C:ASP221 4.8 10.6 1.0 O C:PRO226 4.9 16.0 1.0

Calcium binding site 9 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca803 b:89.0 occ:1.00 OD2 C:ASP622 2.6 121.1 1.0 N C:SER644 2.6 109.8 1.0 O C:VAL645 2.7 110.8 1.0 CD C:GLN643 2.8 103.6 1.0 N C:VAL645 2.9 110.8 1.0 CG C:GLN643 3.0 103.6 1.0 N C:GLN643 3.2 103.6 1.0 OE1 C:GLN643 3.2 103.6 1.0 NE2 C:GLN643 3.2 103.6 1.0 OD2 C:ASP733 3.4 107.1 1.0 CA C:SER644 3.5 109.8 1.0 C C:GLN643 3.5 103.6 1.0 C C:SER644 3.5 109.8 1.0 C C:VAL645 3.6 110.8 1.0 CA C:GLN643 3.6 103.6 1.0 CG C:ASP622 3.7 121.1 1.0 CB C:GLN643 3.8 103.6 1.0 CA C:VAL645 3.9 110.8 1.0 N C:LEU642 3.9 96.5 1.0 CB C:SER644 3.9 109.8 1.0 OD1 C:ASP622 4.1 121.1 1.0 CG C:ASP733 4.2 107.1 1.0 C C:GLY641 4.2 101.4 1.0 CA C:GLY641 4.3 101.4 1.0 C C:LEU642 4.3 96.5 1.0 OD1 C:ASP733 4.3 107.1 1.0 O C:ASN620 4.4 111.7 1.0 CA C:LEU642 4.6 96.5 1.0 OG C:SER644 4.6 109.8 1.0 O C:SER644 4.7 109.8 1.0 O C:GLN643 4.7 103.6 1.0 CG2 C:VAL645 4.8 110.8 1.0 N C:ALA646 4.8 111.2 1.0 CB C:LEU642 4.9 96.5 1.0 CB C:ASP622 4.9 121.1 1.0 CB C:VAL645 4.9 110.8 1.0 O C:GLY641 5.0 101.4 1.0

Calcium binding site 10 out of 21 in the Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Clostridium Perfringens Iota Toxin Pore Ib in Prepore VI State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:26.7 occ:1.00 O D:GLU262 2.3 13.9 1.0 OE2 D:GLU230 2.3 18.9 1.0 OD2 D:ASP223 2.4 13.6 1.0 OD2 D:ASP221 2.4 15.6 1.0 OD2 D:ASP272 2.8 8.1 1.0 CG D:ASP223 3.1 13.6 1.0 CD D:GLU230 3.2 18.9 1.0 O D:SER259 3.3 19.4 1.0 C D:GLU262 3.3 13.9 1.0 OE1 D:GLU230 3.4 18.9 1.0 CG D:ASP221 3.5 15.6 1.0 CB D:ASP223 3.6 13.6 1.0 CA D:SER263 3.6 29.0 1.0 CG D:ASP272 3.8 8.1 1.0 O D:SER263 3.8 29.0 1.0 N D:SER263 3.9 29.0 1.0 C D:SER263 4.0 29.0 1.0 OD1 D:ASP223 4.0 13.6 1.0 CB D:ASP221 4.2 15.6 1.0 CA D:CA802 4.4 23.9 1.0 N D:GLU262 4.4 13.9 1.0 CB D:ASP272 4.4 8.1 1.0 OD1 D:ASP221 4.5 15.6 1.0 CA D:GLU262 4.5 13.9 1.0 C D:SER259 4.5 19.4 1.0 CG D:GLU230 4.6 18.9 1.0 OD1 D:ASP272 4.7 8.1 1.0 CA D:TYR260 4.8 22.1 1.0 CB D:SER263 4.9 29.0 1.0 OG1 D:THR265 4.9 12.5 1.0 C D:TYR260 5.0 22.1 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.