Calcium in PDB 6v1s: Structure of the Clostridioides Difficile Transferase Toxin

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

Binding sites:

The binding sites of Calcium atom in the Structure of the Clostridioides Difficile Transferase Toxin (pdb code 6v1s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Structure of the Clostridioides Difficile Transferase Toxin, PDB code: 6v1s:
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 Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:57.6 occ:1.00 OD2 A:ASP273 2.4 46.4 1.0 OE2 A:GLU231 2.4 56.8 1.0 O A:GLU263 2.5 49.3 1.0 OD2 A:ASP224 2.5 55.4 1.0 O A:ASN260 2.6 54.5 1.0 OD2 A:ASP222 2.6 58.7 1.0 O A:SER264 3.3 48.1 1.0 CD A:GLU231 3.4 56.8 1.0 CG A:ASP273 3.6 46.4 1.0 CG A:ASP224 3.6 55.4 1.0 C A:GLU263 3.7 49.3 1.0 CG A:ASP222 3.7 58.7 1.0 C A:ASN260 3.8 54.5 1.0 OE1 A:GLU231 3.8 56.8 1.0 C A:SER264 4.0 48.1 1.0 CA A:SER264 4.2 48.1 1.0 CB A:ASP222 4.3 58.7 1.0 OD1 A:ASP224 4.3 55.4 1.0 CA A:CA902 4.4 64.7 1.0 N A:SER264 4.4 48.1 1.0 CA A:TYR261 4.4 56.3 1.0 OD1 A:ASP273 4.5 46.4 1.0 CB A:ASP273 4.5 46.4 1.0 N A:TYR261 4.6 56.3 1.0 CB A:ASP224 4.6 55.4 1.0 N A:GLU263 4.7 49.3 1.0 OD1 A:ASP222 4.7 58.7 1.0 CG A:GLU231 4.7 56.8 1.0 CA A:ASN260 4.8 54.5 1.0 CA A:GLU263 4.8 49.3 1.0 C A:TYR261 4.8 56.3 1.0 N A:ASN260 4.8 54.5 1.0 CB A:SER259 4.9 53.7 1.0 N A:LEU262 4.9 54.3 1.0 CD1 A:ILE226 5.0 55.8 1.0

Calcium binding site 2 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:64.7 occ:1.00 OD1 A:ASP224 2.3 55.4 1.0 OE1 A:GLU231 2.3 56.8 1.0 OD1 A:ASP220 2.4 61.0 1.0 OD1 A:ASP222 2.4 58.7 1.0 O A:ILE226 2.6 55.8 1.0 OD2 A:ASP222 2.7 58.7 1.0 CG A:ASP222 2.9 58.7 1.0 CG A:ASP224 3.1 55.4 1.0 OD2 A:ASP224 3.2 55.4 1.0 CD A:GLU231 3.2 56.8 1.0 CG A:ASP220 3.3 61.0 1.0 OE2 A:GLU231 3.5 56.8 1.0 CG1 A:ILE226 3.6 55.8 1.0 OD2 A:ASP220 3.6 61.0 1.0 C A:ILE226 3.7 55.8 1.0 CD1 A:ILE226 4.1 55.8 1.0 OD1 A:ASP228 4.3 59.6 1.0 N A:ILE226 4.3 55.8 1.0 CB A:ASP222 4.4 58.7 1.0 CG A:GLU231 4.4 56.8 1.0 CA A:CA901 4.4 57.6 1.0 CA A:ILE226 4.4 55.8 1.0 CB A:ILE226 4.5 55.8 1.0 CB A:GLU231 4.5 56.8 1.0 CB A:ASP224 4.5 55.4 1.0 N A:ASP224 4.5 55.4 1.0 O A:PRO227 4.5 59.6 1.0 C A:PRO227 4.6 59.6 1.0 CA A:TYR261 4.7 56.3 1.0 CB A:ASP220 4.7 61.0 1.0 N A:PRO227 4.8 59.6 1.0 N A:ASP222 4.8 58.7 1.0 O A:TYR261 4.9 56.3 1.0 CB A:TYR261 4.9 56.3 1.0 N A:ASN223 4.9 58.0 1.0 CA A:ASP224 4.9 55.4 1.0 CA A:PRO227 4.9 59.6 1.0

Calcium binding site 3 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:46.2 occ:1.00 OD2 B:ASP222 2.3 47.5 1.0 O B:GLU263 2.4 44.4 1.0 OD2 B:ASP224 2.4 46.6 1.0 OE2 B:GLU231 2.4 50.9 1.0 O B:ASN260 2.8 46.8 1.0 OD2 B:ASP273 2.9 40.9 1.0 CD B:GLU231 3.4 50.9 1.0 CG B:ASP222 3.5 47.5 1.0 C B:GLU263 3.6 44.4 1.0 CG B:ASP224 3.6 46.6 1.0 C B:ASN260 3.7 46.8 1.0 OE1 B:GLU231 3.8 50.9 1.0 CG B:ASP273 4.0 40.9 1.0 N B:GLU263 4.1 44.4 1.0 CB B:ASP222 4.2 47.5 1.0 CA B:TYR261 4.3 48.4 1.0 N B:TYR261 4.4 48.4 1.0 OD1 B:ASP224 4.4 46.6 1.0 CA B:GLU263 4.4 44.4 1.0 OD1 B:ASP222 4.5 47.5 1.0 CB B:ASP273 4.5 40.9 1.0 CG B:GLU231 4.5 50.9 1.0 N B:SER264 4.6 41.5 1.0 C B:TYR261 4.6 48.4 1.0 CB B:ASP224 4.6 46.6 1.0 N B:LEU262 4.6 48.7 1.0 CA B:SER264 4.7 41.5 1.0 CA B:ASN260 4.7 46.8 1.0 CB B:ASN260 4.8 46.8 1.0 C B:SER264 4.9 41.5 1.0 OD1 B:ASP273 4.9 40.9 1.0 N B:ASN260 4.9 46.8 1.0

Calcium binding site 4 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:47.4 occ:1.00 OD1 B:ASP222 2.3 47.5 1.0 O B:ILE226 2.4 48.7 1.0 N B:THR221 3.4 45.0 1.0 C B:ILE226 3.4 48.7 1.0 CG B:ASP222 3.5 47.5 1.0 O B:ASP224 3.7 46.6 1.0 CA B:PRO227 3.7 50.9 1.0 OE1 B:GLU231 3.9 50.9 1.0 C B:PRO227 3.9 50.9 1.0 N B:PRO227 4.0 50.9 1.0 N B:ASP222 4.0 47.5 1.0 O B:ASP222 4.0 47.5 1.0 OD2 B:ASP222 4.2 47.5 1.0 O B:PRO227 4.3 50.9 1.0 N B:ASP228 4.3 51.9 1.0 C B:ASP222 4.3 47.5 1.0 N B:ILE226 4.4 48.7 1.0 CA B:ILE226 4.5 48.7 1.0 CA B:ASP222 4.5 47.5 1.0 C B:ASP224 4.6 46.6 1.0 CA B:THR221 4.6 45.0 1.0 CB B:ASP222 4.6 47.5 1.0 CD B:GLU231 4.6 50.9 1.0 C B:THR221 4.7 45.0 1.0 N B:ASP224 4.8 46.6 1.0 CB B:ASP224 4.9 46.6 1.0 CG1 B:ILE226 4.9 48.7 1.0 CA B:ASP228 5.0 51.9 1.0 CA B:ASP224 5.0 46.6 1.0

Calcium binding site 5 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:58.6 occ:1.00 OE2 C:GLU231 2.3 56.2 1.0 O C:GLU263 2.4 47.6 1.0 OD2 C:ASP273 2.5 43.6 1.0 O C:ASN260 2.6 53.6 1.0 OD2 C:ASP224 2.6 54.6 1.0 CD C:GLU231 3.3 56.2 1.0 CG C:ASP224 3.6 54.6 1.0 C C:GLU263 3.6 47.6 1.0 CG C:ASP273 3.6 43.6 1.0 O C:SER264 3.7 46.2 1.0 OE1 C:GLU231 3.7 56.2 1.0 C C:ASN260 3.7 53.6 1.0 CA C:CA902 3.8 59.5 1.0 CB C:ASP224 4.0 54.6 1.0 CA C:SER264 4.3 46.2 1.0 C C:SER264 4.3 46.2 1.0 CB C:ASP273 4.3 43.6 1.0 N C:GLU263 4.3 47.6 1.0 N C:SER264 4.4 46.2 1.0 CG C:GLU231 4.4 56.2 1.0 CA C:TYR261 4.5 55.9 1.0 OD1 C:ASP273 4.5 43.6 1.0 N C:TYR261 4.6 55.9 1.0 OD1 C:ASP224 4.6 54.6 1.0 N C:ASN260 4.6 53.6 1.0 CA C:GLU263 4.6 47.6 1.0 CA C:ASN260 4.7 53.6 1.0 C C:TYR261 4.8 55.9 1.0 N C:LEU262 4.8 54.5 1.0 CB C:SER259 4.9 52.6 1.0

Calcium binding site 6 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca902 b:59.5 occ:1.00 OD2 C:ASP224 2.4 54.6 1.0 OD1 C:ASP224 2.5 54.6 1.0 CG C:ASP224 2.7 54.6 1.0 CA C:CA901 3.8 58.6 1.0 O C:GLU263 3.9 47.6 1.0 OE1 C:GLU231 3.9 56.2 1.0 O C:TYR261 4.0 55.9 1.0 CB C:ASP224 4.2 54.6 1.0 C C:TYR261 4.2 55.9 1.0 C C:LEU262 4.6 54.5 1.0 OE2 C:GLU231 4.6 56.2 1.0 CD C:GLU231 4.6 56.2 1.0 N C:ASP224 4.6 54.6 1.0 C C:GLU263 4.6 47.6 1.0 CA C:TYR261 4.7 55.9 1.0 N C:LEU262 4.7 54.5 1.0 N C:GLU263 4.7 47.6 1.0 O C:LEU262 4.8 54.5 1.0 O C:ILE226 4.8 53.4 1.0 CA C:LEU262 4.9 54.5 1.0 O C:ASN260 4.9 53.6 1.0

Calcium binding site 7 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca901 b:40.8 occ:1.00 OD2 D:ASP224 2.3 40.6 1.0 OD2 D:ASP273 2.3 32.1 1.0 OE2 D:GLU231 2.4 41.8 1.0 O D:ASN260 2.4 38.9 1.0 O D:GLU263 2.7 38.5 1.0 OD2 D:ASP222 3.0 41.2 1.0 CG D:ASP273 3.4 32.1 1.0 CD D:GLU231 3.4 41.8 1.0 C D:ASN260 3.5 38.9 1.0 CG D:ASP224 3.5 40.6 1.0 C D:GLU263 3.9 38.5 1.0 CG D:ASP222 4.0 41.2 1.0 CB D:ASP273 4.0 32.1 1.0 OE1 D:GLU231 4.1 41.8 1.0 CA D:TYR261 4.2 39.4 1.0 OD1 D:ASP224 4.2 40.6 1.0 N D:TYR261 4.2 39.4 1.0 OD1 D:ASP273 4.3 32.1 1.0 CA D:CA902 4.4 43.9 1.0 CG D:GLU231 4.4 41.8 1.0 N D:GLU263 4.5 38.5 1.0 CA D:ASN260 4.5 38.9 1.0 CB D:ASP224 4.5 40.6 1.0 CB D:ASP222 4.6 41.2 1.0 N D:ASN260 4.6 38.9 1.0 C D:TYR261 4.7 39.4 1.0 C D:SER264 4.8 35.3 1.0 N D:LEU262 4.8 36.6 1.0 CA D:GLU263 4.8 38.5 1.0 O D:SER264 4.8 35.3 1.0 CB D:ASN260 4.9 38.9 1.0 CA D:SER264 4.9 35.3 1.0 N D:SER264 4.9 35.3 1.0 OD1 D:ASP222 4.9 41.2 1.0

Calcium binding site 8 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:43.9 occ:1.00 O D:ILE226 2.3 39.4 1.0 OD1 D:ASP224 2.3 40.6 1.0 OE1 D:GLU231 2.3 41.8 1.0 OD2 D:ASP222 2.3 41.2 1.0 OD1 D:ASP222 2.3 41.2 1.0 OD1 D:ASP220 2.4 41.9 1.0 CG D:ASP222 2.6 41.2 1.0 CD D:GLU231 2.9 41.8 1.0 OE2 D:GLU231 3.0 41.8 1.0 CG D:ASP224 3.2 40.6 1.0 CG D:ASP220 3.4 41.9 1.0 OD2 D:ASP224 3.4 40.6 1.0 C D:ILE226 3.4 39.4 1.0 OD2 D:ASP220 3.7 41.9 1.0 N D:ILE226 4.0 39.4 1.0 CA D:ILE226 4.1 39.4 1.0 CB D:ASP222 4.1 41.2 1.0 CB D:ILE226 4.2 39.4 1.0 CG D:GLU231 4.3 41.8 1.0 CA D:CA901 4.4 40.8 1.0 N D:PRO227 4.5 42.3 1.0 N D:ASP224 4.5 40.6 1.0 C D:PRO227 4.6 42.3 1.0 OD1 D:ASP228 4.6 43.7 1.0 CB D:ASP224 4.6 40.6 1.0 CG2 D:ILE226 4.6 39.4 1.0 O D:PRO227 4.7 42.3 1.0 CA D:PRO227 4.7 42.3 1.0 CB D:ASP220 4.7 41.9 1.0 CA D:TYR261 4.8 39.4 1.0 N D:ASP222 4.8 41.2 1.0 N D:ASN223 4.9 41.9 1.0 CA D:ASP224 4.9 40.6 1.0 CA D:ASP222 4.9 41.2 1.0 N D:ASP228 5.0 43.7 1.0 CB D:GLU231 5.0 41.8 1.0 C D:ASP224 5.0 40.6 1.0 CA D:ASP220 5.0 41.9 1.0

Calcium binding site 9 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca901 b:32.9 occ:1.00 OE2 E:GLU231 2.3 32.2 1.0 OD2 E:ASP273 2.4 26.5 1.0 O E:GLU263 2.4 31.8 1.0 OD2 E:ASP224 2.4 31.0 1.0 OD2 E:ASP222 3.0 31.4 1.0 O E:ASN260 3.1 32.8 1.0 CD E:GLU231 3.3 32.2 1.0 CG E:ASP224 3.3 31.0 1.0 CB E:ASP224 3.4 31.0 1.0 CG E:ASP273 3.5 26.5 1.0 OE1 E:GLU231 3.5 32.2 1.0 C E:GLU263 3.6 31.8 1.0 CG E:ASP222 4.0 31.4 1.0 CA E:SER264 4.2 27.6 1.0 C E:ASN260 4.3 32.8 1.0 O E:SER264 4.3 27.6 1.0 CB E:ASP273 4.4 26.5 1.0 C E:SER264 4.4 27.6 1.0 N E:SER264 4.4 27.6 1.0 OD1 E:ASP273 4.4 26.5 1.0 OD1 E:ASP222 4.4 31.4 1.0 OD1 E:ASP224 4.5 31.0 1.0 CA E:CA902 4.5 37.4 1.0 CG E:GLU231 4.6 32.2 1.0 CA E:TYR261 4.6 31.8 1.0 N E:GLU263 4.7 31.8 1.0 CA E:GLU263 4.8 31.8 1.0 CA E:ASP224 4.9 31.0 1.0 C E:TYR261 4.9 31.8 1.0 N E:TYR261 5.0 31.8 1.0

Calcium binding site 10 out of 14 in the Structure of the Clostridioides Difficile Transferase Toxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the Clostridioides Difficile Transferase Toxin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca902 b:37.4 occ:1.00 OD2 E:ASP224 2.3 31.0 1.0 OD1 E:ASP224 2.4 31.0 1.0 OD1 E:ASP220 2.4 36.4 1.0 O E:ILE226 2.5 30.7 1.0 OD1 E:ASP222 2.6 31.4 1.0 CG E:ASP224 2.7 31.0 1.0 OE1 E:GLU231 2.7 32.2 1.0 CG E:ASP222 3.6 31.4 1.0 CG E:ASP220 3.7 36.4 1.0 C E:ILE226 3.7 30.7 1.0 CD E:GLU231 3.8 32.2 1.0 OD1 E:ASP228 3.9 35.4 1.0 OD2 E:ASP222 3.9 31.4 1.0 CB E:ASP224 4.2 31.0 1.0 OE2 E:GLU231 4.3 32.2 1.0 N E:ILE226 4.3 30.7 1.0 O E:ASP222 4.4 31.4 1.0 CA E:ILE226 4.4 30.7 1.0 CB E:ASP220 4.5 36.4 1.0 O E:TYR261 4.5 31.8 1.0 CA E:CA901 4.5 32.9 1.0 OD2 E:ASP220 4.5 36.4 1.0 CA E:ASP220 4.5 36.4 1.0 C E:PRO227 4.6 35.0 1.0 N E:ASP222 4.6 31.4 1.0 O E:PRO227 4.6 35.0 1.0 CB E:ILE226 4.6 30.7 1.0 N E:THR221 4.6 31.3 1.0 N E:PRO227 4.7 35.0 1.0 CA E:PRO227 4.7 35.0 1.0 C E:ASP220 4.8 36.4 1.0 N E:ASP224 4.8 31.0 1.0 CA E:TYR261 4.9 31.8 1.0 C E:ASP222 4.9 31.4 1.0 CG E:ASP228 4.9 35.4 1.0 CB E:ASP222 4.9 31.4 1.0 CB E:GLU231 4.9 32.2 1.0 CB E:TYR261 5.0 31.8 1.0 CA E:ASP224 5.0 31.0 1.0 CG E:GLU231 5.0 32.2 1.0

M.J.Sheedlo, D.M.Anderson, A.K.Thomas, D.B.Lacy. Structural Elucidation of Theclostridioides Difficiletransferase Toxin Reveals A Single-Site Binding Mode For the Enzyme. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 32123082
DOI: 10.1073/PNAS.1920555117