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Calcium in PDB 9mdi: Clostridioides Difficile Transferase B Component Dimer

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 9mdi

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Calcium binding site 1 out of 6 in the Clostridioides Difficile Transferase B Component Dimer


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:69.5
occ:1.00
 OE1 A:GLU231 2.4 76.0 1.0
OE2 A:GLU231 2.4 76.0 1.0
OD2 A:ASP224 2.5 76.8 1.0
OD2 A:ASP222 2.8 77.4 1.0
CD A:GLU231 2.8 76.0 1.0
OD2 A:ASP273 2.8 56.6 1.0
O A:GLU263 3.0 73.7 1.0
CG A:ASP224 3.5 76.8 1.0
CG A:ASP222 3.8 77.4 1.0
CA A:CA902 3.8 76.5 1.0
O A:ASN260 3.8 69.8 1.0
CG A:ASP273 3.9 56.6 1.0
OD1 A:ASP224 4.0 76.8 1.0
C A:GLU263 4.0 73.7 1.0
CB A:ASP222 4.1 77.4 1.0
CA A:TYR261 4.2 71.6 1.0
OD1 A:ASP273 4.3 56.6 1.0
CG A:GLU231 4.3 76.0 1.0
OG A:SER259 4.4 67.0 1.0
C A:ASN260 4.4 69.8 1.0
O A:SER264 4.4 65.9 1.0
CA A:SER264 4.4 65.9 1.0
C A:TYR261 4.5 71.6 1.0
N A:TYR261 4.6 71.6 1.0
O A:TYR261 4.7 71.6 1.0
N A:SER264 4.7 65.9 1.0
C A:SER264 4.7 65.9 1.0
CB A:ASP224 4.7 76.8 1.0
N A:GLU263 4.8 73.7 1.0
OD1 A:ASP222 4.9 77.4 1.0

Calcium binding site 2 out of 6 in 9mdi

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Calcium binding site 2 out of 6 in the Clostridioides Difficile Transferase B Component Dimer


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:76.5
occ:1.00
 OE2 A:GLU231 2.4 76.0 1.0
OD1 A:ASP224 2.5 76.8 1.0
O A:ILE226 2.5 75.3 1.0
OD2 A:ASP224 2.6 76.8 1.0
CG A:ASP224 2.7 76.8 1.0
CD A:GLU231 3.3 76.0 1.0
C A:ILE226 3.7 75.3 1.0
CA A:CA901 3.8 69.5 1.0
CG A:GLU231 3.9 76.0 1.0
O A:ASP224 3.9 76.8 1.0
CB A:ASP224 4.0 76.8 1.0
OE1 A:GLU231 4.2 76.0 1.0
O A:PRO227 4.3 79.8 1.0
C A:PRO227 4.3 79.8 1.0
OD1 A:ASP220 4.4 83.1 1.0
C A:ASP224 4.4 76.8 1.0
N A:ASP222 4.5 77.4 1.0
OD2 A:ASP222 4.6 77.4 1.0
CA A:PRO227 4.6 79.8 1.0
CA A:ILE226 4.6 75.3 1.0
N A:PRO227 4.6 79.8 1.0
N A:ILE226 4.6 75.3 1.0
CA A:ASP224 4.6 76.8 1.0
CB A:ASP222 4.7 77.4 1.0
N A:ASP228 4.7 82.7 1.0
N A:ASP224 4.8 76.8 1.0
N A:THR221 4.8 78.2 1.0
CG A:ASP222 4.8 77.4 1.0
CB A:ILE226 4.8 75.3 1.0

Calcium binding site 3 out of 6 in 9mdi

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Calcium binding site 3 out of 6 in the Clostridioides Difficile Transferase B Component Dimer


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:59.6
occ:1.00
 O A:ASN621 2.4 54.7 1.0
OD2 A:ASP734 2.4 53.6 1.0
OD1 A:ASP734 2.5 53.6 1.0
O A:SER646 2.5 71.1 1.0
CG A:ASP734 2.8 53.6 1.0
O A:GLN644 3.3 66.6 1.0
C A:ASN621 3.5 54.7 1.0
C A:SER646 3.6 71.1 1.0
CB A:ASN621 3.9 54.7 1.0
CA A:ASN621 4.0 54.7 1.0
C A:GLN644 4.1 66.6 1.0
CB A:ASP734 4.3 53.6 1.0
N A:SER646 4.3 71.1 1.0
ND2 A:ASN735 4.4 49.7 1.0
N A:GLN644 4.4 66.6 1.0
N A:ALA647 4.5 69.2 1.0
CA A:ALA647 4.5 69.2 1.0
CA A:SER646 4.5 71.1 1.0
N A:PHE622 4.6 58.1 1.0
CA A:GLN644 4.6 66.6 1.0
CB A:GLN644 4.7 66.6 1.0
CG A:ASN621 4.8 54.7 1.0
CB A:PHE622 4.8 58.1 1.0
C A:GLY645 4.8 71.5 1.0
CD2 A:PHE622 4.8 58.1 1.0
OD2 A:ASP623 4.9 65.4 1.0
O A:PHE622 4.9 58.1 1.0

Calcium binding site 4 out of 6 in 9mdi

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Calcium binding site 4 out of 6 in the Clostridioides Difficile Transferase B Component Dimer


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:58.4
occ:1.00
 CA B:CA902 2.2 75.1 1.0
OE2 B:GLU231 2.4 66.2 1.0
OD2 B:ASP222 2.4 79.5 1.0
OD2 B:ASP224 2.4 73.7 1.0
OD2 B:ASP273 2.5 54.5 1.0
O B:ASN260 2.7 67.5 1.0
OE1 B:GLU231 2.7 66.2 1.0
CD B:GLU231 2.8 66.2 1.0
O B:GLU263 3.3 73.0 1.0
OG B:SER259 3.4 61.7 1.0
CG B:ASP222 3.6 79.5 1.0
CG B:ASP224 3.6 73.7 1.0
CG B:ASP273 3.7 54.5 1.0
C B:ASN260 3.9 67.5 1.0
OD1 B:ASP224 4.0 73.7 1.0
O B:SER264 4.1 66.2 1.0
CB B:ASP273 4.1 54.5 1.0
CG B:GLU231 4.1 66.2 1.0
OD1 B:ASP222 4.2 79.5 1.0
C B:GLU263 4.4 73.0 1.0
CA B:TYR261 4.4 75.2 1.0
CA B:SER264 4.4 66.2 1.0
OG1 B:THR266 4.5 57.1 1.0
C B:SER264 4.5 66.2 1.0
CB B:SER259 4.5 61.7 1.0
N B:TYR261 4.6 75.2 1.0
CB B:ASP222 4.7 79.5 1.0
OD1 B:ASP273 4.7 54.5 1.0
CB B:ASP224 4.8 73.7 1.0
N B:SER264 4.9 66.2 1.0
N B:ASN260 4.9 67.5 1.0

Calcium binding site 5 out of 6 in 9mdi

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Calcium binding site 5 out of 6 in the Clostridioides Difficile Transferase B Component Dimer


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:75.1
occ:1.00
 CA B:CA901 2.2 58.4 1.0
OE1 B:GLU231 2.4 66.2 1.0
OD2 B:ASP222 2.4 79.5 1.0
OE2 B:GLU231 2.4 66.2 1.0
OD2 B:ASP224 2.4 73.7 1.0
OD1 B:ASP224 2.5 73.7 1.0
CD B:GLU231 2.7 66.2 1.0
CG B:ASP224 2.8 73.7 1.0
CG B:ASP222 2.9 79.5 1.0
OD1 B:ASP222 2.9 79.5 1.0
O B:ILE226 3.6 70.5 1.0
O B:ASP222 4.0 79.5 1.0
CG B:GLU231 4.2 66.2 1.0
CB B:ASP222 4.2 79.5 1.0
O B:ASN260 4.2 67.5 1.0
CB B:ILE226 4.2 70.5 1.0
CB B:ASP224 4.3 73.7 1.0
OD2 B:ASP273 4.5 54.5 1.0
CG2 B:ILE226 4.5 70.5 1.0
OD1 B:ASP220 4.5 86.7 1.0
C B:ILE226 4.6 70.5 1.0
CA B:TYR261 4.7 75.2 1.0
C B:ASP222 4.7 79.5 1.0
CA B:ILE226 4.8 70.5 1.0
O B:GLU263 4.8 73.0 1.0
CB B:GLU231 4.8 66.2 1.0
N B:ILE226 4.9 70.5 1.0
N B:ASP224 4.9 73.7 1.0
CA B:ASP222 4.9 79.5 1.0

Calcium binding site 6 out of 6 in 9mdi

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


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 Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:85.7
occ:1.00
 O B:GLN644 2.5 93.4 1.0
OD1 B:ASP734 2.5 78.1 1.0
O B:ASN621 2.6 78.0 1.0
OD2 B:ASP734 2.8 78.1 1.0
O B:SER646 3.0 92.1 1.0
CG B:ASP734 3.0 78.1 1.0
C B:ASN621 3.6 78.0 1.0
OD1 B:ASN735 3.6 72.8 1.0
CB B:ASN621 3.6 78.0 1.0
C B:GLN644 3.6 93.4 1.0
CA B:ASN621 3.9 78.0 1.0
C B:SER646 4.2 92.1 1.0
CA B:GLN644 4.4 93.4 1.0
N B:GLN644 4.4 93.4 1.0
CB B:GLN644 4.5 93.4 1.0
CB B:ASP734 4.5 78.1 1.0
N B:SER646 4.6 92.1 1.0
C B:GLY645 4.6 96.1 1.0
N B:GLY645 4.7 96.1 1.0
CG B:ASN735 4.7 72.8 1.0
CG B:ASN621 4.7 78.0 1.0
CA B:GLY645 4.8 96.1 1.0
N B:PHE622 4.8 81.5 1.0
N B:ASN735 5.0 72.8 1.0
O B:GLY645 5.0 96.1 1.0

Reference:

M.J.Sheedlo, R.M.Mullard. Oligomerization of the Clostridioides Difficile Transferase B Component Proceeds Through A Stepwise Mechanism in Vitro To Be Published.
Page generated: Mon Aug 4 18:56:38 2025

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