Calcium in PDB 8ekm: Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A (pdb code 8ekm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A, PDB code: 8ekm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:72.0 occ:1.00 OD2 A:ASP222 2.3 83.2 1.0 OD2 A:ASP273 2.3 69.1 1.0 OE1 A:GLU231 2.4 76.7 1.0 OD2 A:ASP224 2.5 81.4 1.0 OE2 A:GLU231 2.6 76.7 1.0 O A:ASN260 2.8 74.2 1.0 CD A:GLU231 2.8 76.7 1.0 O A:GLU263 3.0 74.0 1.0 CG A:ASP222 3.5 83.2 1.0 CG A:ASP273 3.5 69.1 1.0 CG A:ASP224 3.7 81.4 1.0 CA A:CA902 3.8 82.7 1.0 C A:ASN260 3.9 74.2 1.0 CA A:TYR261 4.1 77.4 1.0 C A:GLU263 4.1 74.0 1.0 OD1 A:ASP224 4.1 81.4 1.0 CB A:ASP222 4.1 83.2 1.0 CB A:ASP273 4.2 69.1 1.0 O A:SER264 4.2 69.1 1.0 CG A:GLU231 4.3 76.7 1.0 OD1 A:ASP222 4.4 83.2 1.0 N A:TYR261 4.5 77.4 1.0 OD1 A:ASP273 4.5 69.1 1.0 CA A:SER264 4.6 69.1 1.0 C A:TYR261 4.6 77.4 1.0 C A:SER264 4.6 69.1 1.0 OG1 A:THR266 4.8 67.1 1.0 N A:SER264 4.8 69.1 1.0 N A:GLU263 4.9 74.0 1.0 CB A:ASP224 4.9 81.4 1.0 OG A:SER259 5.0 69.7 1.0

Calcium binding site 2 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:82.7 occ:1.00 OD1 A:ASP222 2.2 83.2 1.0 OE2 A:GLU231 2.3 76.7 1.0 O A:ILE226 2.3 77.5 1.0 OD2 A:ASP222 2.4 83.2 1.0 OD1 A:ASP224 2.4 81.4 1.0 CG A:ASP222 2.6 83.2 1.0 OD1 A:ASP220 2.9 88.7 1.0 CD A:GLU231 2.9 76.7 1.0 CG A:ASP224 3.3 81.4 1.0 CG A:GLU231 3.5 76.7 1.0 OD2 A:ASP224 3.5 81.4 1.0 C A:ILE226 3.5 77.5 1.0 OE1 A:GLU231 3.7 76.7 1.0 CA A:CA901 3.8 72.0 1.0 C A:PRO227 4.1 79.9 1.0 N A:ASP228 4.1 81.6 1.0 CG A:ASP220 4.1 88.7 1.0 CB A:ASP222 4.1 83.2 1.0 CA A:PRO227 4.3 79.9 1.0 O A:PRO227 4.4 79.9 1.0 N A:PRO227 4.4 79.9 1.0 CA A:ILE226 4.5 77.5 1.0 CB A:GLU231 4.5 76.7 1.0 CA A:ASP228 4.5 81.6 1.0 O A:TYR261 4.5 77.4 1.0 CA A:TYR261 4.6 77.4 1.0 N A:ASP222 4.6 83.2 1.0 CB A:ILE226 4.6 77.5 1.0 CB A:ASP228 4.6 81.6 1.0 CB A:TYR261 4.6 77.4 1.0 N A:ILE226 4.6 77.5 1.0 CB A:ASP224 4.7 81.4 1.0 OD2 A:ASP220 4.8 88.7 1.0 CA A:ASP220 4.8 88.7 1.0 CA A:ASP222 4.9 83.2 1.0 N A:ASP224 4.9 81.4 1.0 C A:TYR261 4.9 77.4 1.0 N A:THR221 5.0 86.2 1.0

Calcium binding site 3 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:81.2 occ:1.00 OD1 B:ASP222 2.2 81.1 1.0 O B:ILE226 2.3 76.3 1.0 OE2 B:GLU231 2.3 74.8 1.0 OD1 B:ASP224 2.4 80.8 1.0 OD1 B:ASP220 2.4 86.2 1.0 OD2 B:ASP222 2.8 81.1 1.0 CG B:ASP222 2.8 81.1 1.0 CG B:ASP224 3.3 80.8 1.0 CD B:GLU231 3.4 74.8 1.0 OD2 B:ASP224 3.5 80.8 1.0 C B:ILE226 3.5 76.3 1.0 CG B:ASP220 3.6 86.2 1.0 N B:ASP228 4.1 83.7 1.0 OE1 B:GLU231 4.1 74.8 1.0 C B:PRO227 4.1 79.3 1.0 CA B:CA902 4.2 70.1 1.0 CG B:GLU231 4.3 74.8 1.0 CB B:ASP222 4.3 81.1 1.0 OD2 B:ASP220 4.3 86.2 1.0 CA B:ILE226 4.4 76.3 1.0 N B:PRO227 4.4 79.3 1.0 CA B:PRO227 4.4 79.3 1.0 N B:ILE226 4.4 76.3 1.0 N B:ASP222 4.5 81.1 1.0 CB B:ASP228 4.5 83.7 1.0 CB B:ILE226 4.5 76.3 1.0 CA B:ASP228 4.5 83.7 1.0 CA B:ASP220 4.5 86.2 1.0 O B:PRO227 4.6 79.3 1.0 CB B:ASP224 4.7 80.8 1.0 CB B:ASP220 4.7 86.2 1.0 N B:ASP224 4.7 80.8 1.0 N B:THR221 4.8 84.0 1.0 O B:TYR261 4.8 76.5 1.0 CA B:ASP222 4.9 81.1 1.0 CB B:GLU231 5.0 74.8 1.0 N B:ASN223 5.0 84.4 1.0 C B:ASP220 5.0 86.2 1.0

Calcium binding site 4 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:70.1 occ:1.00 OD2 B:ASP273 2.3 67.0 1.0 OD2 B:ASP222 2.3 81.1 1.0 OE1 B:GLU231 2.4 74.8 1.0 OD2 B:ASP224 2.4 80.8 1.0 OE2 B:GLU231 2.8 74.8 1.0 O B:GLU263 2.9 72.2 1.0 CD B:GLU231 2.9 74.8 1.0 O B:ASN260 3.1 73.1 1.0 CG B:ASP222 3.4 81.1 1.0 CG B:ASP273 3.4 67.0 1.0 CG B:ASP224 3.6 80.8 1.0 CB B:ASP273 4.0 67.0 1.0 C B:GLU263 4.0 72.2 1.0 CB B:ASP222 4.1 81.1 1.0 OD1 B:ASP224 4.2 80.8 1.0 C B:ASN260 4.2 73.1 1.0 O B:SER264 4.2 65.8 1.0 CA B:CA901 4.2 81.2 1.0 CA B:TYR261 4.3 76.5 1.0 CG B:GLU231 4.3 74.8 1.0 OD1 B:ASP222 4.4 81.1 1.0 CA B:SER264 4.5 65.8 1.0 OD1 B:ASP273 4.5 67.0 1.0 C B:SER264 4.6 65.8 1.0 N B:SER264 4.7 65.8 1.0 N B:TYR261 4.7 76.5 1.0 CB B:ASP224 4.7 80.8 1.0 C B:TYR261 4.8 76.5 1.0 OG1 B:THR266 4.8 65.0 1.0 N B:GLU263 4.9 72.2 1.0

Calcium binding site 5 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:77.2 occ:1.00 OD1 C:ASP222 2.2 80.0 1.0 OE2 C:GLU231 2.3 74.2 1.0 O C:ILE226 2.3 75.2 1.0 OD1 C:ASP224 2.4 79.3 1.0 OD2 C:ASP222 2.5 80.0 1.0 CG C:ASP222 2.7 80.0 1.0 OD1 C:ASP220 2.8 84.7 1.0 CD C:GLU231 3.0 74.2 1.0 CG C:ASP224 3.3 79.3 1.0 OD2 C:ASP224 3.5 79.3 1.0 CG C:GLU231 3.5 74.2 1.0 C C:ILE226 3.5 75.2 1.0 OE1 C:GLU231 3.8 74.2 1.0 CA C:CA902 3.8 69.8 1.0 C C:PRO227 4.0 77.1 1.0 CG C:ASP220 4.1 84.7 1.0 N C:ASP228 4.1 78.4 1.0 CB C:ASP222 4.2 80.0 1.0 CA C:PRO227 4.3 77.1 1.0 N C:PRO227 4.4 77.1 1.0 O C:PRO227 4.4 77.1 1.0 CA C:ASP228 4.5 78.4 1.0 CB C:GLU231 4.5 74.2 1.0 CA C:ILE226 4.5 75.2 1.0 O C:TYR261 4.5 74.8 1.0 N C:ASP222 4.6 80.0 1.0 CB C:ASP228 4.6 78.4 1.0 CA C:TYR261 4.6 74.8 1.0 CB C:ILE226 4.6 75.2 1.0 CB C:TYR261 4.6 74.8 1.0 N C:ILE226 4.7 75.2 1.0 CB C:ASP224 4.7 79.3 1.0 OD2 C:ASP220 4.8 84.7 1.0 CA C:ASP220 4.8 84.7 1.0 CA C:ASP222 4.9 80.0 1.0 N C:ASP224 4.9 79.3 1.0 C C:TYR261 5.0 74.8 1.0

Calcium binding site 6 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca902 b:69.8 occ:1.00 OD2 C:ASP222 2.3 80.0 1.0 OD2 C:ASP273 2.3 67.8 1.0 OE1 C:GLU231 2.4 74.2 1.0 OE2 C:GLU231 2.5 74.2 1.0 OD2 C:ASP224 2.6 79.3 1.0 CD C:GLU231 2.8 74.2 1.0 O C:ASN260 2.8 72.5 1.0 O C:GLU263 3.0 72.5 1.0 CG C:ASP222 3.5 80.0 1.0 CG C:ASP273 3.5 67.8 1.0 CG C:ASP224 3.7 79.3 1.0 CA C:CA901 3.8 77.2 1.0 C C:ASN260 3.9 72.5 1.0 CA C:TYR261 4.0 74.8 1.0 CB C:ASP273 4.1 67.8 1.0 C C:GLU263 4.1 72.5 1.0 CB C:ASP222 4.2 80.0 1.0 OD1 C:ASP224 4.2 79.3 1.0 CG C:GLU231 4.3 74.2 1.0 O C:SER264 4.4 68.0 1.0 OD1 C:ASP222 4.4 80.0 1.0 N C:TYR261 4.4 74.8 1.0 OD1 C:ASP273 4.5 67.8 1.0 C C:TYR261 4.5 74.8 1.0 CA C:SER264 4.7 68.0 1.0 OG1 C:THR266 4.7 66.5 1.0 C C:SER264 4.7 68.0 1.0 N C:GLU263 4.8 72.5 1.0 N C:SER264 4.9 68.0 1.0 CB C:ASP224 5.0 79.3 1.0 O C:TYR261 5.0 74.8 1.0 OG C:SER259 5.0 69.0 1.0

Calcium binding site 7 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca901 b:81.5 occ:1.00 OD1 D:ASP222 2.2 81.3 1.0 OE2 D:GLU231 2.3 75.0 1.0 O D:ILE226 2.3 75.9 1.0 OD1 D:ASP220 2.4 86.5 1.0 OD1 D:ASP224 2.4 80.3 1.0 OD2 D:ASP222 2.6 81.3 1.0 CG D:ASP222 2.8 81.3 1.0 CD D:GLU231 3.1 75.0 1.0 CG D:ASP224 3.3 80.3 1.0 CG D:ASP220 3.4 86.5 1.0 OD2 D:ASP224 3.4 80.3 1.0 C D:ILE226 3.5 75.9 1.0 CG D:GLU231 3.6 75.0 1.0 OD2 D:ASP220 3.6 86.5 1.0 CA D:CA902 3.9 70.8 1.0 OE1 D:GLU231 4.1 75.0 1.0 N D:ASP228 4.1 79.0 1.0 C D:PRO227 4.1 77.3 1.0 CB D:ASP222 4.2 81.3 1.0 CA D:ILE226 4.4 75.9 1.0 CB D:ILE226 4.5 75.9 1.0 N D:PRO227 4.5 77.3 1.0 CA D:ASP228 4.5 79.0 1.0 N D:ILE226 4.5 75.9 1.0 O D:PRO227 4.5 77.3 1.0 CA D:PRO227 4.5 77.3 1.0 CB D:ASP228 4.5 79.0 1.0 N D:ASP222 4.6 81.3 1.0 O D:TYR261 4.7 74.9 1.0 CB D:GLU231 4.7 75.0 1.0 CB D:ASP224 4.7 80.3 1.0 CB D:ASP220 4.7 86.5 1.0 CA D:TYR261 4.7 74.9 1.0 CB D:TYR261 4.8 74.9 1.0 N D:ASP224 4.9 80.3 1.0 CA D:ASP222 4.9 81.3 1.0 N D:THR221 5.0 84.2 1.0 CA D:ASP220 5.0 86.5 1.0

Calcium binding site 8 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:70.8 occ:1.00 OD2 D:ASP222 2.3 81.3 1.0 OD2 D:ASP273 2.3 66.9 1.0 OE1 D:GLU231 2.4 75.0 1.0 OE2 D:GLU231 2.4 75.0 1.0 OD2 D:ASP224 2.6 80.3 1.0 CD D:GLU231 2.7 75.0 1.0 O D:ASN260 2.7 72.2 1.0 O D:GLU263 3.1 72.5 1.0 CG D:ASP222 3.5 81.3 1.0 CG D:ASP273 3.5 66.9 1.0 CG D:ASP224 3.7 80.3 1.0 C D:ASN260 3.9 72.2 1.0 CA D:CA901 3.9 81.5 1.0 CA D:TYR261 4.1 74.9 1.0 CB D:ASP273 4.1 66.9 1.0 OD1 D:ASP224 4.2 80.3 1.0 C D:GLU263 4.2 72.5 1.0 CG D:GLU231 4.2 75.0 1.0 CB D:ASP222 4.3 81.3 1.0 O D:SER264 4.4 67.5 1.0 OD1 D:ASP222 4.4 81.3 1.0 N D:TYR261 4.4 74.9 1.0 OD1 D:ASP273 4.5 66.9 1.0 C D:TYR261 4.6 74.9 1.0 CA D:SER264 4.7 67.5 1.0 OG1 D:THR266 4.8 66.8 1.0 C D:SER264 4.8 67.5 1.0 OG D:SER259 4.8 68.7 1.0 CB D:ASP224 4.9 80.3 1.0 N D:SER264 4.9 67.5 1.0 N D:GLU263 5.0 72.5 1.0 CB D:GLU231 5.0 75.0 1.0

Calcium binding site 9 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca901 b:84.4 occ:1.00 OD1 E:ASP222 2.2 83.2 1.0 OE2 E:GLU231 2.3 78.3 1.0 O E:ILE226 2.3 78.0 1.0 OD1 E:ASP224 2.4 81.1 1.0 OD2 E:ASP222 2.5 83.2 1.0 OD1 E:ASP220 2.5 88.0 1.0 CG E:ASP222 2.7 83.2 1.0 CD E:GLU231 3.0 78.3 1.0 CG E:ASP224 3.2 81.1 1.0 OD2 E:ASP224 3.3 81.1 1.0 C E:ILE226 3.5 78.0 1.0 CG E:ASP220 3.6 88.0 1.0 OE1 E:GLU231 3.7 78.3 1.0 CG E:GLU231 3.8 78.3 1.0 OD1 E:ASP228 3.9 84.5 1.0 CA E:CA902 3.9 69.7 1.0 OD2 E:ASP220 4.1 88.0 1.0 CB E:ASP222 4.1 83.2 1.0 C E:PRO227 4.3 81.3 1.0 CA E:ILE226 4.4 78.0 1.0 O E:PRO227 4.4 81.3 1.0 N E:PRO227 4.4 81.3 1.0 CA E:PRO227 4.4 81.3 1.0 CB E:ILE226 4.5 78.0 1.0 N E:ILE226 4.5 78.0 1.0 N E:ASP222 4.5 83.2 1.0 N E:ASP228 4.5 84.5 1.0 CB E:ASP224 4.6 81.1 1.0 O E:TYR261 4.7 79.6 1.0 CA E:TYR261 4.7 79.6 1.0 CB E:GLU231 4.7 78.3 1.0 CB E:TYR261 4.8 79.6 1.0 N E:ASP224 4.8 81.1 1.0 CA E:ASP222 4.8 83.2 1.0 CB E:ASP220 4.9 88.0 1.0 CA E:ASP228 4.9 84.5 1.0 N E:THR221 4.9 86.1 1.0 CA E:ASP220 5.0 88.0 1.0

Calcium binding site 10 out of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Clostridioides Difficile Binary Toxin Translocase Cdtb Double Mutant - D623A D734A within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca902 b:69.7 occ:1.00 OD2 E:ASP273 2.3 69.3 1.0 OD2 E:ASP222 2.3 83.2 1.0 OE1 E:GLU231 2.4 78.3 1.0 O E:ASN260 2.6 75.5 1.0 OE2 E:GLU231 2.8 78.3 1.0 OD2 E:ASP224 2.8 81.1 1.0 O E:GLU263 2.9 73.7 1.0 CD E:GLU231 2.9 78.3 1.0 CG E:ASP273 3.5 69.3 1.0 CG E:ASP222 3.5 83.2 1.0 C E:ASN260 3.7 75.5 1.0 CA E:CA901 3.9 84.4 1.0 CG E:ASP224 4.0 81.1 1.0 C E:GLU263 4.1 73.7 1.0 CA E:TYR261 4.1 79.6 1.0 CB E:ASP273 4.1 69.3 1.0 CB E:ASP222 4.2 83.2 1.0 O E:SER264 4.3 68.8 1.0 N E:TYR261 4.3 79.6 1.0 CG E:GLU231 4.4 78.3 1.0 OD1 E:ASP224 4.4 81.1 1.0 OD1 E:ASP222 4.4 83.2 1.0 OD1 E:ASP273 4.5 69.3 1.0 OG1 E:THR266 4.5 66.9 1.0 C E:TYR261 4.6 79.6 1.0 CA E:SER264 4.6 68.8 1.0 C E:SER264 4.7 68.8 1.0 N E:GLU263 4.8 73.7 1.0 N E:SER264 4.8 68.8 1.0 N E:ASN260 4.8 75.5 1.0 OG E:SER259 4.8 72.3 1.0 CA E:ASN260 4.9 75.5 1.0 N E:LEU262 5.0 77.3 1.0

D.L.Abeyawardhane, K.A.Adipietro, R.G.Ruiz, K.M.Varney, R.R.Rustandi, V.I.Silin, E.Pozharski, D.J.Weber. Calcium-Mediated Pore Formation of Clostridioides Difficile Binary Toxin To Be Published.