Calcium in PDB 9mdr: Clostridioides Difficile Transferase B Component Symmetric Heptamer

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

Binding sites:

The binding sites of Calcium atom in the Clostridioides Difficile Transferase B Component Symmetric Heptamer (pdb code 9mdr). 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 Transferase B Component Symmetric Heptamer, PDB code: 9mdr:
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 Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:41.9 occ:1.00 O A:GLU263 2.4 54.2 1.0 OE2 A:GLU231 2.4 57.3 1.0 OD2 A:ASP273 2.4 60.5 1.0 OD2 A:ASP224 2.4 73.9 1.0 OD2 A:ASP222 2.6 71.4 1.0 O A:ASN260 2.8 67.9 1.0 CD A:GLU231 3.3 58.7 1.0 CG A:ASP273 3.5 61.0 1.0 CG A:ASP224 3.6 71.3 1.0 C A:GLU263 3.6 64.3 1.0 OE1 A:GLU231 3.7 62.1 1.0 CG A:ASP222 3.7 71.4 1.0 O A:SER264 3.9 67.6 1.0 OD1 A:ASN260 4.0 76.1 1.0 C A:ASN260 4.0 67.2 1.0 CB A:ASP273 4.1 45.0 1.0 OD1 A:ASP224 4.1 65.6 1.0 CB A:ASP222 4.2 68.2 1.0 C A:SER264 4.2 62.5 1.0 CA A:CA902 4.3 40.8 1.0 CA A:SER264 4.4 57.6 1.0 N A:SER264 4.5 59.3 1.0 N A:GLU263 4.5 69.6 1.0 OD1 A:ASP273 4.5 62.7 1.0 CG A:GLU231 4.6 53.4 1.0 CA A:TYR261 4.6 56.5 1.0 CA A:GLU263 4.6 64.1 1.0 OG1 A:THR266 4.7 56.9 1.0 N A:TYR261 4.7 57.4 1.0 CB A:ASP224 4.8 62.4 1.0 OD1 A:ASP222 4.8 70.0 1.0 C A:TYR261 4.9 58.8 1.0 N A:ASN260 5.0 60.3 1.0

Calcium binding site 2 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:40.8 occ:1.00 OD1 A:ASP222 2.3 70.0 1.0 O A:ILE226 2.4 65.5 1.0 OD1 A:ASP224 2.4 65.6 1.0 OD2 A:ASP222 2.4 71.4 1.0 OE1 A:GLU231 2.4 62.1 1.0 CG A:ASP222 2.7 71.4 1.0 OD1 A:ASP220 3.1 66.1 1.0 C A:ILE226 3.4 64.0 1.0 CG A:ASP224 3.4 71.3 1.0 CD A:GLU231 3.5 58.7 1.0 OD2 A:ASP224 3.7 73.9 1.0 CB A:ILE226 3.7 59.6 1.0 CA A:ILE226 3.9 63.5 1.0 OE2 A:GLU231 3.9 57.3 1.0 OD1 A:ASP228 4.0 68.0 1.0 N A:ILE226 4.0 69.4 1.0 CG2 A:ILE226 4.1 58.4 1.0 CB A:ASP222 4.1 68.2 1.0 CG A:ASP220 4.2 65.3 1.0 CA A:CA901 4.3 41.9 1.0 N A:PRO227 4.5 55.2 1.0 O A:PRO227 4.5 71.1 1.0 N A:ASP224 4.5 72.0 1.0 C A:PRO227 4.5 60.7 1.0 N A:ASP222 4.7 72.7 1.0 CB A:ASP224 4.7 62.4 1.0 N A:ASN223 4.7 65.0 1.0 CA A:TYR261 4.8 56.5 1.0 CG A:GLU231 4.8 53.4 1.0 CA A:PRO227 4.8 58.3 1.0 CA A:ASP220 4.8 65.1 1.0 CB A:GLU231 4.9 48.0 1.0 CA A:ASP222 4.9 66.1 1.0 O A:TYR261 4.9 63.1 1.0 N A:ASP228 4.9 59.0 1.0 OD2 A:ASP220 4.9 67.6 1.0 CB A:TYR261 5.0 58.6 1.0 CG1 A:ILE226 5.0 59.3 1.0 CA A:ASP224 5.0 67.0 1.0

Calcium binding site 3 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:46.4 occ:1.00 O B:GLU263 2.4 54.2 1.0 OE2 B:GLU231 2.4 57.3 1.0 OD2 B:ASP224 2.4 73.9 1.0 OD2 B:ASP273 2.4 60.5 1.0 OD2 B:ASP222 2.6 71.4 1.0 O B:ASN260 2.8 67.9 1.0 CD B:GLU231 3.3 58.7 1.0 CG B:ASP273 3.5 61.0 1.0 CG B:ASP224 3.6 71.3 1.0 C B:GLU263 3.6 64.3 1.0 OE1 B:GLU231 3.7 62.1 1.0 CG B:ASP222 3.7 71.4 1.0 O B:SER264 3.9 67.6 1.0 OD1 B:ASN260 4.0 76.1 1.0 C B:ASN260 4.0 67.2 1.0 CB B:ASP273 4.1 45.0 1.0 OD1 B:ASP224 4.1 65.6 1.0 CB B:ASP222 4.2 68.2 1.0 C B:SER264 4.3 62.5 1.0 CA B:CA902 4.3 41.0 1.0 CA B:SER264 4.4 57.6 1.0 N B:SER264 4.5 59.3 1.0 N B:GLU263 4.5 69.6 1.0 OD1 B:ASP273 4.5 62.7 1.0 CA B:TYR261 4.6 56.5 1.0 CG B:GLU231 4.6 53.4 1.0 CA B:GLU263 4.6 64.1 1.0 OG1 B:THR266 4.7 56.9 1.0 N B:TYR261 4.7 57.4 1.0 CB B:ASP224 4.8 62.4 1.0 OD1 B:ASP222 4.8 70.0 1.0 C B:TYR261 4.9 58.8 1.0 N B:ASN260 5.0 60.3 1.0

Calcium binding site 4 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:41.0 occ:1.00 OD1 B:ASP222 2.3 70.0 1.0 O B:ILE226 2.4 65.5 1.0 OD1 B:ASP224 2.4 65.6 1.0 OD2 B:ASP222 2.4 71.4 1.0 OE1 B:GLU231 2.4 62.1 1.0 CG B:ASP222 2.7 71.4 1.0 OD1 B:ASP220 3.1 66.1 1.0 CG B:ASP224 3.4 71.3 1.0 C B:ILE226 3.4 64.0 1.0 CD B:GLU231 3.5 58.7 1.0 OD2 B:ASP224 3.7 73.9 1.0 CB B:ILE226 3.7 59.6 1.0 CA B:ILE226 3.9 63.5 1.0 OE2 B:GLU231 3.9 57.3 1.0 OD1 B:ASP228 4.0 68.0 1.0 N B:ILE226 4.0 69.4 1.0 CG2 B:ILE226 4.1 58.4 1.0 CB B:ASP222 4.1 68.2 1.0 CG B:ASP220 4.2 65.3 1.0 CA B:CA901 4.3 46.4 1.0 N B:PRO227 4.5 55.2 1.0 N B:ASP224 4.5 72.0 1.0 O B:PRO227 4.5 71.1 1.0 C B:PRO227 4.5 60.7 1.0 N B:ASP222 4.7 72.7 1.0 CB B:ASP224 4.7 62.4 1.0 N B:ASN223 4.7 65.0 1.0 CA B:TYR261 4.8 56.5 1.0 CG B:GLU231 4.8 53.4 1.0 CA B:PRO227 4.8 58.3 1.0 CA B:ASP222 4.9 66.1 1.0 CA B:ASP220 4.9 65.1 1.0 CB B:GLU231 4.9 48.0 1.0 O B:TYR261 4.9 63.1 1.0 N B:ASP228 4.9 59.0 1.0 OD2 B:ASP220 4.9 67.6 1.0 CB B:TYR261 5.0 58.6 1.0 CA B:ASP224 5.0 67.0 1.0 CG1 B:ILE226 5.0 59.3 1.0

Calcium binding site 5 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:36.9 occ:1.00 O C:GLU263 2.4 54.2 1.0 OE2 C:GLU231 2.4 57.3 1.0 OD2 C:ASP224 2.4 73.9 1.0 OD2 C:ASP273 2.4 60.5 1.0 OD2 C:ASP222 2.6 71.4 1.0 O C:ASN260 2.8 67.9 1.0 CD C:GLU231 3.3 58.7 1.0 CG C:ASP273 3.5 61.0 1.0 CG C:ASP224 3.6 71.3 1.0 C C:GLU263 3.6 64.3 1.0 OE1 C:GLU231 3.7 62.1 1.0 CG C:ASP222 3.7 71.4 1.0 O C:SER264 3.9 67.6 1.0 OD1 C:ASN260 4.0 76.1 1.0 C C:ASN260 4.0 67.2 1.0 CB C:ASP273 4.1 45.0 1.0 OD1 C:ASP224 4.1 65.6 1.0 CB C:ASP222 4.2 68.2 1.0 C C:SER264 4.2 62.5 1.0 CA C:CA902 4.3 41.0 1.0 CA C:SER264 4.3 57.6 1.0 N C:SER264 4.4 59.3 1.0 N C:GLU263 4.5 69.6 1.0 OD1 C:ASP273 4.5 62.7 1.0 CG C:GLU231 4.6 53.4 1.0 CA C:TYR261 4.6 56.5 1.0 CA C:GLU263 4.6 64.1 1.0 OG1 C:THR266 4.7 56.9 1.0 CB C:ASP224 4.7 62.4 1.0 N C:TYR261 4.8 57.4 1.0 OD1 C:ASP222 4.8 70.0 1.0 C C:TYR261 4.9 58.8 1.0

Calcium binding site 6 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca902 b:41.0 occ:1.00 OD1 C:ASP222 2.3 70.0 1.0 OD1 C:ASP224 2.4 65.6 1.0 O C:ILE226 2.4 65.5 1.0 OD2 C:ASP222 2.4 71.4 1.0 OE1 C:GLU231 2.4 62.1 1.0 CG C:ASP222 2.7 71.4 1.0 OD1 C:ASP220 3.1 66.1 1.0 CG C:ASP224 3.4 71.3 1.0 C C:ILE226 3.4 64.0 1.0 CD C:GLU231 3.5 58.7 1.0 OD2 C:ASP224 3.7 73.9 1.0 CB C:ILE226 3.7 59.6 1.0 CA C:ILE226 3.9 63.5 1.0 OE2 C:GLU231 3.9 57.3 1.0 OD1 C:ASP228 4.0 68.0 1.0 N C:ILE226 4.0 69.4 1.0 CG2 C:ILE226 4.1 58.4 1.0 CB C:ASP222 4.1 68.2 1.0 CG C:ASP220 4.2 65.3 1.0 CA C:CA901 4.3 36.9 1.0 N C:ASP224 4.5 72.0 1.0 N C:PRO227 4.5 55.2 1.0 O C:PRO227 4.5 71.1 1.0 C C:PRO227 4.5 60.7 1.0 N C:ASP222 4.7 72.7 1.0 CB C:ASP224 4.7 62.4 1.0 N C:ASN223 4.7 65.0 1.0 CA C:TYR261 4.8 56.5 1.0 CG C:GLU231 4.8 53.4 1.0 CA C:PRO227 4.8 58.3 1.0 CA C:ASP222 4.9 66.1 1.0 CA C:ASP220 4.9 65.1 1.0 CB C:GLU231 4.9 48.0 1.0 O C:TYR261 4.9 63.1 1.0 N C:ASP228 4.9 59.0 1.0 OD2 C:ASP220 4.9 67.6 1.0 CB C:TYR261 5.0 58.6 1.0 CA C:ASP224 5.0 67.0 1.0 CG1 C:ILE226 5.0 59.3 1.0

Calcium binding site 7 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca901 b:41.9 occ:1.00 O D:GLU263 2.4 54.2 1.0 OE2 D:GLU231 2.4 57.3 1.0 OD2 D:ASP273 2.4 60.5 1.0 OD2 D:ASP224 2.4 73.9 1.0 OD2 D:ASP222 2.7 71.4 1.0 O D:ASN260 2.8 67.9 1.0 CD D:GLU231 3.3 58.7 1.0 CG D:ASP273 3.5 61.0 1.0 CG D:ASP224 3.6 71.3 1.0 C D:GLU263 3.6 64.3 1.0 OE1 D:GLU231 3.7 62.1 1.0 CG D:ASP222 3.8 71.4 1.0 O D:SER264 3.9 67.6 1.0 OD1 D:ASN260 4.0 76.1 1.0 C D:ASN260 4.0 67.2 1.0 CB D:ASP273 4.0 45.0 1.0 OD1 D:ASP224 4.1 65.6 1.0 CB D:ASP222 4.2 68.2 1.0 C D:SER264 4.2 62.5 1.0 CA D:SER264 4.3 57.6 1.0 CA D:CA902 4.4 44.2 1.0 N D:SER264 4.4 59.3 1.0 N D:GLU263 4.5 69.6 1.0 OD1 D:ASP273 4.5 62.7 1.0 CG D:GLU231 4.6 53.4 1.0 CA D:TYR261 4.6 56.5 1.0 CA D:GLU263 4.6 64.1 1.0 OG1 D:THR266 4.7 56.9 1.0 CB D:ASP224 4.7 62.4 1.0 N D:TYR261 4.8 57.4 1.0 OD1 D:ASP222 4.8 70.0 1.0 C D:TYR261 4.9 58.8 1.0

Calcium binding site 8 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:44.2 occ:1.00 OD1 D:ASP222 2.3 70.0 1.0 O D:ILE226 2.4 65.5 1.0 OD1 D:ASP224 2.4 65.6 1.0 OD2 D:ASP222 2.4 71.4 1.0 OE1 D:GLU231 2.4 62.1 1.0 CG D:ASP222 2.7 71.4 1.0 OD1 D:ASP220 3.0 66.1 1.0 CG D:ASP224 3.4 71.3 1.0 C D:ILE226 3.4 64.0 1.0 CD D:GLU231 3.5 58.7 1.0 OD2 D:ASP224 3.7 73.9 1.0 CB D:ILE226 3.7 59.6 1.0 CA D:ILE226 3.9 63.5 1.0 OE2 D:GLU231 3.9 57.3 1.0 OD1 D:ASP228 4.0 68.0 1.0 N D:ILE226 4.0 69.4 1.0 CG2 D:ILE226 4.1 58.4 1.0 CB D:ASP222 4.1 68.2 1.0 CG D:ASP220 4.2 65.3 1.0 CA D:CA901 4.4 41.9 1.0 N D:PRO227 4.5 55.2 1.0 N D:ASP224 4.5 72.0 1.0 O D:PRO227 4.5 71.1 1.0 C D:PRO227 4.5 60.7 1.0 N D:ASP222 4.7 72.7 1.0 CB D:ASP224 4.7 62.4 1.0 N D:ASN223 4.7 65.0 1.0 CA D:TYR261 4.8 56.5 1.0 CG D:GLU231 4.8 53.4 1.0 CA D:PRO227 4.8 58.3 1.0 CA D:ASP222 4.9 66.1 1.0 CA D:ASP220 4.9 65.1 1.0 CB D:GLU231 4.9 48.0 1.0 O D:TYR261 4.9 63.1 1.0 N D:ASP228 4.9 59.0 1.0 OD2 D:ASP220 4.9 67.6 1.0 CB D:TYR261 5.0 58.6 1.0 CA D:ASP224 5.0 67.0 1.0 CG1 D:ILE226 5.0 59.3 1.0

Calcium binding site 9 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca901 b:73.7 occ:1.00 O E:GLU263 2.4 54.2 1.0 OD2 E:ASP224 2.4 73.9 1.0 OD2 E:ASP273 2.4 60.5 1.0 OE2 E:GLU231 2.4 57.3 1.0 OD2 E:ASP222 2.7 71.4 1.0 O E:ASN260 2.8 67.9 1.0 CD E:GLU231 3.3 58.7 1.0 CG E:ASP273 3.5 61.0 1.0 CG E:ASP224 3.5 71.3 1.0 C E:GLU263 3.6 64.3 1.0 OE1 E:GLU231 3.7 62.1 1.0 CG E:ASP222 3.8 71.4 1.0 O E:SER264 3.9 67.6 1.0 OD1 E:ASN260 4.0 76.1 1.0 CB E:ASP273 4.0 45.0 1.0 C E:ASN260 4.0 67.2 1.0 OD1 E:ASP224 4.1 65.6 1.0 CB E:ASP222 4.2 68.2 1.0 C E:SER264 4.2 62.5 1.0 CA E:SER264 4.3 57.6 1.0 CA E:CA902 4.4 70.7 1.0 N E:SER264 4.4 59.3 1.0 N E:GLU263 4.5 69.6 1.0 OD1 E:ASP273 4.5 62.7 1.0 CG E:GLU231 4.6 53.4 1.0 CA E:TYR261 4.6 56.5 1.0 CA E:GLU263 4.6 64.1 1.0 OG1 E:THR266 4.7 56.9 1.0 CB E:ASP224 4.7 62.4 1.0 N E:TYR261 4.8 57.4 1.0 OD1 E:ASP222 4.8 70.0 1.0 C E:TYR261 4.9 58.8 1.0

Calcium binding site 10 out of 14 in the Clostridioides Difficile Transferase B Component Symmetric Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Clostridioides Difficile Transferase B Component Symmetric Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca902 b:70.7 occ:1.00 OD1 E:ASP222 2.3 70.0 1.0 OD1 E:ASP224 2.4 65.6 1.0 O E:ILE226 2.4 65.5 1.0 OD2 E:ASP222 2.4 71.4 1.0 OE1 E:GLU231 2.4 62.1 1.0 CG E:ASP222 2.7 71.4 1.0 OD1 E:ASP220 3.0 66.1 1.0 CG E:ASP224 3.4 71.3 1.0 C E:ILE226 3.4 64.0 1.0 CD E:GLU231 3.5 58.7 1.0 OD2 E:ASP224 3.7 73.9 1.0 CB E:ILE226 3.7 59.6 1.0 CA E:ILE226 3.9 63.5 1.0 OE2 E:GLU231 3.9 57.3 1.0 OD1 E:ASP228 4.0 68.0 1.0 N E:ILE226 4.0 69.4 1.0 CG2 E:ILE226 4.1 58.4 1.0 CB E:ASP222 4.1 68.2 1.0 CG E:ASP220 4.2 65.3 1.0 CA E:CA901 4.4 73.7 1.0 N E:ASP224 4.5 72.0 1.0 N E:PRO227 4.5 55.2 1.0 O E:PRO227 4.5 71.1 1.0 C E:PRO227 4.5 60.7 1.0 N E:ASP222 4.7 72.7 1.0 CB E:ASP224 4.7 62.4 1.0 N E:ASN223 4.7 65.0 1.0 CA E:TYR261 4.8 56.5 1.0 CG E:GLU231 4.8 53.4 1.0 CA E:PRO227 4.8 58.3 1.0 CA E:ASP222 4.9 66.1 1.0 CA E:ASP220 4.9 65.1 1.0 CB E:GLU231 4.9 48.0 1.0 O E:TYR261 4.9 63.1 1.0 N E:ASP228 4.9 59.0 1.0 OD2 E:ASP220 4.9 67.6 1.0 CA E:ASP224 5.0 67.0 1.0 CB E:TYR261 5.0 58.6 1.0 CG1 E:ILE226 5.0 59.3 1.0

M.J.Sheedlo, R.M.Mullard. Oligomerization of the Clostridioides Difficile Transferase B Component Proceeds Through A Stepwise Mechanism in Vitro To Be Published.