Calcium in PDB 9mdl: Clostridioides Difficile Transferase B Component Trimer

The binding sites of Calcium atom in the Clostridioides Difficile Transferase B Component Trimer (pdb code 9mdl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Clostridioides Difficile Transferase B Component Trimer, PDB code: 9mdl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:75.0 occ:1.00 OE2 A:GLU231 2.4 83.0 1.0 OD2 A:ASP273 2.5 75.7 1.0 O A:ASN260 2.7 71.4 1.0 O A:GLU263 2.9 77.1 1.0 CD A:GLU231 3.4 83.0 1.0 CG A:ASP273 3.5 75.7 1.0 C A:ASN260 3.6 71.4 1.0 OD2 A:ASP222 3.7 92.0 1.0 OD2 A:ASP224 3.7 91.2 1.0 OE1 A:GLU231 3.8 83.0 1.0 O A:SER264 4.0 74.7 1.0 C A:GLU263 4.1 77.1 1.0 OG1 A:THR266 4.2 65.8 1.0 CB A:ASP273 4.3 75.7 1.0 OD1 A:ASP273 4.3 75.7 1.0 C A:SER264 4.4 74.7 1.0 CA A:ASN260 4.4 71.4 1.0 N A:TYR261 4.4 80.2 1.0 CB A:ASN260 4.4 71.4 1.0 CA A:SER264 4.5 74.7 1.0 CA A:TYR261 4.5 80.2 1.0 N A:ASN260 4.5 71.4 1.0 OG A:SER259 4.6 69.2 1.0 CG A:GLU231 4.7 83.0 1.0 CG A:ASP222 4.7 92.0 1.0 N A:SER264 4.7 74.7 1.0 CB A:SER259 4.8 69.2 1.0 CG A:ASP224 4.8 91.2 1.0 CD1 A:ILE226 4.9 89.6 1.0

Calcium binding site 2 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:89.2 occ:1.00 OD1 A:ASP228 2.4 92.8 1.0 OE1 A:GLU231 2.5 83.0 1.0 OD1 A:ASP224 3.0 91.2 1.0 N A:ASP222 3.4 92.0 1.0 CD A:GLU231 3.4 83.0 1.0 OD2 A:ASP222 3.5 92.0 1.0 CG A:ASP228 3.6 92.8 1.0 OD2 A:ASP224 3.7 91.2 1.0 CB A:ASP222 3.7 92.0 1.0 CG A:ASP224 3.7 91.2 1.0 O A:ILE226 3.8 89.6 1.0 N A:THR221 3.8 95.8 1.0 CG A:ASP222 3.8 92.0 1.0 OE2 A:GLU231 4.0 83.0 1.0 CA A:ASP222 4.1 92.0 1.0 OD1 A:ASP220 4.1 104.3 1.0 CB A:THR221 4.3 95.8 1.0 C A:THR221 4.3 95.8 1.0 CA A:THR221 4.3 95.8 1.0 N A:ASP228 4.4 92.8 1.0 CG A:GLU231 4.4 83.0 1.0 CA A:ASP228 4.4 92.8 1.0 OD2 A:ASP228 4.4 92.8 1.0 CB A:ASP228 4.5 92.8 1.0 O A:TYR261 4.6 80.2 1.0 C A:ASP222 4.7 92.0 1.0 C A:PRO227 4.7 94.8 1.0 O A:ASP222 4.7 92.0 1.0 OD1 A:ASP222 4.7 92.0 1.0 C A:ASP220 4.9 104.3 1.0 CA A:ASP220 4.9 104.3 1.0 C A:ILE226 4.9 89.6 1.0 CA A:TYR261 5.0 80.2 1.0 CG A:ASP220 5.0 104.3 1.0 OG1 A:THR221 5.0 95.8 1.0

Calcium binding site 3 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:117.2 occ:1.00 O A:GLN644 2.4 98.2 1.0 O A:SER646 2.4 113.2 1.0 OD2 A:ASP734 2.4 95.5 1.0 CG A:ASP734 3.1 95.5 1.0 OD1 A:ASP734 3.1 95.5 1.0 O A:ASN621 3.2 97.3 1.0 C A:GLN644 3.3 98.2 1.0 OD2 A:ASP623 3.4 102.5 1.0 N A:SER646 3.4 113.2 1.0 C A:SER646 3.5 113.2 1.0 N A:GLN644 4.0 98.2 1.0 CA A:SER646 4.1 113.2 1.0 CA A:GLN644 4.1 98.2 1.0 N A:GLY645 4.1 101.6 1.0 C A:GLY645 4.1 101.6 1.0 CA A:GLY645 4.3 101.6 1.0 CG A:ASP623 4.3 102.5 1.0 CB A:GLN644 4.4 98.2 1.0 C A:ASN621 4.4 97.3 1.0 N A:ALA647 4.5 108.5 1.0 CB A:ASP734 4.6 95.5 1.0 OD1 A:ASP623 4.6 102.5 1.0 OE1 A:GLN644 4.7 98.2 1.0 CA A:ALA647 4.9 108.5 1.0 N A:LEU643 5.0 98.3 1.0 CB A:ASN621 5.0 97.3 1.0 ND2 A:ASN735 5.0 84.6 1.0 CB A:SER646 5.0 113.2 1.0 O A:PHE622 5.0 101.3 1.0

Calcium binding site 4 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:73.3 occ:1.00 OD2 B:ASP222 2.4 89.4 1.0 CA B:CA902 2.4 91.0 1.0 OE2 B:GLU231 2.5 87.4 1.0 OD2 B:ASP224 2.6 89.9 1.0 O B:GLU263 3.1 85.4 1.0 OD2 B:ASP273 3.2 65.5 1.0 O B:ASN260 3.2 72.3 1.0 CD B:GLU231 3.4 87.4 1.0 CG B:ASP222 3.5 89.4 1.0 OE1 B:GLU231 3.6 87.4 1.0 CG B:ASP224 3.6 89.9 1.0 CB B:ASP222 3.8 89.4 1.0 C B:GLU263 4.0 85.4 1.0 OD1 B:ASP224 4.0 89.9 1.0 CA B:SER264 4.1 73.6 1.0 CG B:ASP273 4.1 65.5 1.0 OD1 B:ASP273 4.2 65.5 1.0 O B:SER264 4.3 73.6 1.0 C B:ASN260 4.4 72.3 1.0 OG B:SER259 4.4 70.7 1.0 CA B:TYR261 4.4 82.0 1.0 N B:SER264 4.4 73.6 1.0 C B:SER264 4.5 73.6 1.0 OD1 B:ASP222 4.6 89.4 1.0 C B:TYR261 4.7 82.0 1.0 CG B:GLU231 4.8 87.4 1.0 O B:TYR261 4.8 82.0 1.0 CB B:ASP224 4.9 89.9 1.0 N B:TYR261 4.9 82.0 1.0

Calcium binding site 5 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:91.0 occ:1.00 OE1 B:GLU231 2.4 87.4 1.0 CA B:CA901 2.4 73.3 1.0 OD2 B:ASP224 2.5 89.9 1.0 OE2 B:GLU231 2.6 87.4 1.0 CD B:GLU231 2.8 87.4 1.0 OD1 B:ASP224 3.1 89.9 1.0 CG B:ASP224 3.1 89.9 1.0 OD2 B:ASP222 3.6 89.4 1.0 O B:ILE226 3.7 81.0 1.0 CB B:ILE226 3.8 81.0 1.0 CG2 B:ILE226 3.8 81.0 1.0 CG B:GLU231 4.2 87.4 1.0 CB B:ASP222 4.3 89.4 1.0 CG B:ASP222 4.4 89.4 1.0 C B:ILE226 4.4 81.0 1.0 CB B:ASP224 4.5 89.9 1.0 CA B:ILE226 4.6 81.0 1.0 OD2 B:ASP273 4.7 65.5 1.0 O B:ASN260 4.7 72.3 1.0 N B:ILE226 4.8 81.0 1.0 CB B:GLU231 4.8 87.4 1.0 CA B:TYR261 4.9 82.0 1.0 N B:ASP222 4.9 89.4 1.0 O B:PRO227 5.0 87.7 1.0 CG1 B:ILE226 5.0 81.0 1.0

Calcium binding site 6 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:88.4 occ:1.00 O B:ASN621 2.4 81.0 1.0 O B:SER646 2.7 86.4 1.0 OD1 B:ASP734 2.9 70.0 1.0 OD2 B:ASP734 3.0 70.0 1.0 OD2 B:ASP623 3.1 95.9 1.0 CG B:ASP734 3.3 70.0 1.0 C B:ASN621 3.5 81.0 1.0 O B:GLN644 3.6 83.1 1.0 C B:SER646 3.7 86.4 1.0 CB B:ASN621 3.8 81.0 1.0 CG B:ASP623 4.1 95.9 1.0 CA B:ASN621 4.1 81.0 1.0 ND2 B:ASN735 4.3 66.7 1.0 N B:SER646 4.3 86.4 1.0 C B:GLN644 4.4 83.1 1.0 CA B:SER646 4.5 86.4 1.0 OD1 B:ASP623 4.6 95.9 1.0 CG B:ASN621 4.6 81.0 1.0 N B:PHE622 4.7 87.8 1.0 N B:ALA647 4.7 89.2 1.0 ND2 B:ASN621 4.7 81.0 1.0 N B:GLN644 4.8 83.1 1.0 O B:PHE622 4.8 87.8 1.0 CB B:ASP734 4.8 70.0 1.0 CA B:ALA647 4.8 89.2 1.0 CB B:PHE622 4.9 87.8 1.0 C B:PHE622 4.9 87.8 1.0 CB B:SER646 4.9 86.4 1.0 C B:GLY645 4.9 85.5 1.0

Calcium binding site 7 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:90.9 occ:1.00 OE2 C:GLU231 2.4 113.7 1.0 OD2 C:ASP273 2.4 100.1 1.0 O C:ASN260 2.4 99.8 1.0 OD2 C:ASP222 3.1 120.3 1.0 CD C:GLU231 3.2 113.7 1.0 OE1 C:GLU231 3.4 113.7 1.0 CG C:ASP273 3.4 100.1 1.0 O C:GLU263 3.4 101.5 1.0 OD2 C:ASP224 3.4 124.2 1.0 OG C:SER259 3.5 98.3 1.0 C C:ASN260 3.6 99.8 1.0 OD1 C:ASP273 4.1 100.1 1.0 CG C:ASP222 4.2 120.3 1.0 CB C:SER259 4.3 98.3 1.0 CB C:ASP273 4.4 100.1 1.0 O C:SER264 4.4 90.9 1.0 CA C:TYR261 4.4 110.2 1.0 N C:TYR261 4.5 110.2 1.0 CG C:ASP224 4.5 124.2 1.0 N C:ASN260 4.5 99.8 1.0 CA C:ASN260 4.6 99.8 1.0 C C:GLU263 4.6 101.5 1.0 CA C:CA902 4.6 128.2 1.0 CB C:ASP222 4.7 120.3 1.0 CG C:GLU231 4.7 113.7 1.0 CB C:THR266 4.7 80.9 1.0 C C:SER259 4.8 98.3 1.0 C C:SER264 5.0 90.9 1.0 CB C:ASN260 5.0 99.8 1.0

Calcium binding site 8 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca902 b:128.2 occ:1.00 O C:ILE226 2.4 124.9 1.0 OD2 C:ASP224 2.4 124.2 1.0 OE1 C:GLU231 2.5 113.7 1.0 OD1 C:ASP224 2.8 124.2 1.0 CG C:ASP224 2.8 124.2 1.0 CD C:GLU231 2.9 113.7 1.0 CG C:GLU231 3.3 113.7 1.0 C C:ILE226 3.5 124.9 1.0 OE2 C:GLU231 3.7 113.7 1.0 O C:PRO227 3.9 126.0 1.0 OD2 C:ASP220 4.1 141.1 1.0 C C:PRO227 4.1 126.0 1.0 CB C:ASP224 4.2 124.2 1.0 CB C:ILE226 4.3 124.9 1.0 CA C:ILE226 4.3 124.9 1.0 OG1 C:THR221 4.4 134.2 1.0 OD2 C:ASP222 4.4 120.3 1.0 N C:PRO227 4.5 126.0 1.0 N C:ILE226 4.5 124.9 1.0 CA C:PRO227 4.6 126.0 1.0 O C:ASP224 4.6 124.2 1.0 CA C:CA901 4.6 90.9 1.0 CB C:GLU231 4.6 113.7 1.0 N C:ASP228 4.6 122.3 1.0 N C:ASP222 4.6 120.3 1.0 CG2 C:ILE226 4.7 124.9 1.0 CB C:ASP222 4.7 120.3 1.0 CG C:ASP222 4.8 120.3 1.0 C C:ASP224 4.9 124.2 1.0 CA C:ASP228 4.9 122.3 1.0 CG C:ASP220 5.0 141.1 1.0 N C:THR221 5.0 134.2 1.0

Calcium binding site 9 out of 9 in the Clostridioides Difficile Transferase B Component Trimer


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 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca903 b:147.8 occ:1.00 O C:GLN644 2.4 148.3 1.0 OD2 C:ASP623 2.4 138.2 1.0 O C:SER646 2.7 162.8 1.0 OE1 C:GLN644 2.8 148.3 1.0 CD C:GLN644 3.0 148.3 1.0 NE2 C:GLN644 3.1 148.3 1.0 O C:ASN621 3.1 143.8 1.0 OD2 C:ASP734 3.3 141.9 1.0 CG C:ASP623 3.4 138.2 1.0 C C:GLN644 3.6 148.3 1.0 OD1 C:ASP734 3.6 141.9 1.0 OD1 C:ASP623 3.8 138.2 1.0 CG C:GLN644 3.9 148.3 1.0 C C:SER646 3.9 162.8 1.0 CG C:ASP734 3.9 141.9 1.0 N C:SER646 4.0 162.8 1.0 N C:GLN644 4.3 148.3 1.0 C C:ASN621 4.3 143.8 1.0 CA C:GLN644 4.4 148.3 1.0 CB C:ASN621 4.4 143.8 1.0 CA C:SER646 4.6 162.8 1.0 CB C:GLN644 4.6 148.3 1.0 N C:GLY645 4.6 156.5 1.0 C C:GLY645 4.7 156.5 1.0 CB C:ASP623 4.7 138.2 1.0 O C:PHE622 4.8 140.4 1.0 CA C:GLY645 4.8 156.5 1.0 CA C:ASN621 4.9 143.8 1.0 N C:ALA647 4.9 161.6 1.0 ND2 C:ASN621 5.0 143.8 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.