Calcium in PDB 8ekl: Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Calcium atom in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
(pdb code 8ekl). 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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1, PDB code: 8ekl:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 1 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca901
b:66.0
occ:1.00
|
OD1
|
A:ASP222
|
2.2
|
69.3
|
1.0
|
O
|
A:ILE226
|
2.2
|
60.7
|
1.0
|
OE2
|
A:GLU231
|
2.3
|
63.6
|
1.0
|
OD1
|
A:ASP220
|
2.4
|
69.7
|
1.0
|
OD1
|
A:ASP224
|
2.8
|
62.1
|
1.0
|
CG
|
A:ASP222
|
3.1
|
69.3
|
1.0
|
OD2
|
A:ASP222
|
3.3
|
67.0
|
1.0
|
C
|
A:ILE226
|
3.4
|
57.0
|
1.0
|
CD
|
A:GLU231
|
3.5
|
57.8
|
1.0
|
CG
|
A:ASP220
|
3.6
|
70.9
|
1.0
|
O
|
A:PRO227
|
3.8
|
63.8
|
1.0
|
C
|
A:PRO227
|
3.8
|
63.8
|
1.0
|
CG
|
A:ASP224
|
3.8
|
59.1
|
1.0
|
OD1
|
A:ASP228
|
4.0
|
71.0
|
1.0
|
CA
|
A:PRO227
|
4.1
|
61.6
|
1.0
|
OE1
|
A:GLU231
|
4.2
|
59.9
|
1.0
|
N
|
A:ASP228
|
4.2
|
68.4
|
1.0
|
OD2
|
A:ASP224
|
4.2
|
59.1
|
1.0
|
N
|
A:PRO227
|
4.2
|
59.0
|
1.0
|
N
|
A:THR221
|
4.3
|
64.6
|
1.0
|
N
|
A:ASP222
|
4.3
|
66.0
|
1.0
|
CA
|
A:ILE226
|
4.4
|
55.2
|
1.0
|
CB
|
A:ASP220
|
4.5
|
72.0
|
1.0
|
OD2
|
A:ASP220
|
4.5
|
72.6
|
1.0
|
CA
|
A:ASP220
|
4.5
|
72.5
|
1.0
|
CB
|
A:ASP222
|
4.5
|
59.9
|
1.0
|
N
|
A:ILE226
|
4.6
|
53.6
|
1.0
|
CB
|
A:ILE226
|
4.6
|
55.5
|
1.0
|
CA
|
A:ASP228
|
4.6
|
66.2
|
1.0
|
O
|
A:TYR261
|
4.6
|
60.1
|
1.0
|
CG
|
A:GLU231
|
4.7
|
54.5
|
1.0
|
CA
|
A:TYR261
|
4.8
|
51.8
|
1.0
|
N
|
A:ASP224
|
4.8
|
61.1
|
1.0
|
N
|
A:ASN223
|
4.8
|
61.0
|
1.0
|
C
|
A:ASP220
|
4.8
|
73.9
|
1.0
|
CA
|
A:ASP222
|
4.9
|
61.0
|
1.0
|
CA
|
A:CA902
|
4.9
|
48.1
|
1.0
|
CG
|
A:ASP228
|
4.9
|
70.0
|
1.0
|
CB
|
A:TYR261
|
5.0
|
56.8
|
1.0
|
|
Calcium binding site 2 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 2 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca902
b:48.1
occ:1.00
|
OD2
|
A:ASP273
|
2.2
|
53.3
|
1.0
|
OD2
|
A:ASP222
|
2.2
|
67.0
|
1.0
|
O
|
A:GLU263
|
2.3
|
58.4
|
1.0
|
OE1
|
A:GLU231
|
2.3
|
59.9
|
1.0
|
O
|
A:ASN260
|
2.3
|
57.1
|
1.0
|
OD2
|
A:ASP224
|
3.0
|
59.1
|
1.0
|
CD
|
A:GLU231
|
3.4
|
57.8
|
1.0
|
CG
|
A:ASP273
|
3.4
|
50.7
|
1.0
|
CG
|
A:ASP222
|
3.5
|
69.3
|
1.0
|
C
|
A:ASN260
|
3.5
|
49.6
|
1.0
|
C
|
A:GLU263
|
3.5
|
61.0
|
1.0
|
OE2
|
A:GLU231
|
3.8
|
63.6
|
1.0
|
CG
|
A:ASP224
|
4.1
|
59.1
|
1.0
|
OG1
|
A:THR266
|
4.1
|
45.1
|
1.0
|
CB
|
A:ASP273
|
4.1
|
43.1
|
1.0
|
CB
|
A:ASP222
|
4.2
|
59.9
|
1.0
|
N
|
A:ASN260
|
4.3
|
52.0
|
1.0
|
CA
|
A:SER264
|
4.3
|
53.4
|
1.0
|
OD1
|
A:ASP273
|
4.3
|
51.1
|
1.0
|
CA
|
A:TYR261
|
4.3
|
51.8
|
1.0
|
N
|
A:GLU263
|
4.4
|
57.2
|
1.0
|
N
|
A:SER264
|
4.4
|
61.2
|
1.0
|
N
|
A:TYR261
|
4.4
|
52.9
|
1.0
|
OD1
|
A:ASP222
|
4.4
|
69.3
|
1.0
|
OD1
|
A:ASP224
|
4.4
|
62.1
|
1.0
|
CA
|
A:ASN260
|
4.4
|
45.3
|
1.0
|
CB
|
A:SER259
|
4.4
|
46.0
|
1.0
|
CA
|
A:GLU263
|
4.5
|
57.2
|
1.0
|
CG
|
A:GLU231
|
4.6
|
54.5
|
1.0
|
C
|
A:SER264
|
4.6
|
52.2
|
1.0
|
C
|
A:TYR261
|
4.8
|
56.4
|
1.0
|
CB
|
A:ASN260
|
4.9
|
53.0
|
1.0
|
O
|
A:SER264
|
4.9
|
52.0
|
1.0
|
CA
|
A:CA901
|
4.9
|
66.0
|
1.0
|
|
Calcium binding site 3 out
of 14 in 8ekl
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Calcium Binding Sites List in 8ekl
Calcium binding site 3 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca901
b:70.5
occ:1.00
|
OD1
|
B:ASP222
|
2.2
|
70.4
|
1.0
|
O
|
B:ILE226
|
2.3
|
61.7
|
1.0
|
OD1
|
B:ASP220
|
2.3
|
69.8
|
1.0
|
OE1
|
B:GLU231
|
2.3
|
65.8
|
1.0
|
OD1
|
B:ASP224
|
2.6
|
63.4
|
1.0
|
CG
|
B:ASP222
|
3.0
|
69.9
|
1.0
|
OD2
|
B:ASP222
|
3.2
|
66.6
|
1.0
|
C
|
B:ILE226
|
3.5
|
59.6
|
1.0
|
CD
|
B:GLU231
|
3.5
|
58.7
|
1.0
|
CG
|
B:ASP220
|
3.6
|
72.2
|
1.0
|
CG
|
B:ASP224
|
3.7
|
58.6
|
1.0
|
O
|
B:PRO227
|
3.8
|
64.3
|
1.0
|
C
|
B:PRO227
|
4.1
|
64.7
|
1.0
|
OD2
|
B:ASP224
|
4.1
|
57.8
|
1.0
|
OE2
|
B:GLU231
|
4.2
|
60.5
|
1.0
|
CA
|
B:ILE226
|
4.3
|
57.6
|
1.0
|
CB
|
B:ILE226
|
4.4
|
56.3
|
1.0
|
N
|
B:PRO227
|
4.4
|
62.9
|
1.0
|
OD2
|
B:ASP220
|
4.4
|
73.3
|
1.0
|
N
|
B:ILE226
|
4.4
|
54.9
|
1.0
|
N
|
B:ASP222
|
4.4
|
67.7
|
1.0
|
CA
|
B:PRO227
|
4.4
|
62.3
|
1.0
|
CB
|
B:ASP220
|
4.4
|
72.8
|
1.0
|
O
|
B:ASP224
|
4.5
|
69.8
|
1.0
|
CB
|
B:ASP222
|
4.5
|
61.4
|
1.0
|
N
|
B:THR221
|
4.5
|
67.5
|
1.0
|
N
|
B:ASP224
|
4.5
|
62.4
|
1.0
|
CA
|
B:ASP220
|
4.5
|
72.8
|
1.0
|
CG
|
B:GLU231
|
4.7
|
56.8
|
1.0
|
N
|
B:ASP228
|
4.7
|
72.3
|
1.0
|
N
|
B:ASN223
|
4.8
|
61.8
|
1.0
|
C
|
B:ASP224
|
4.9
|
67.0
|
1.0
|
CA
|
B:CA902
|
4.9
|
48.4
|
1.0
|
CA
|
B:ASP222
|
4.9
|
61.5
|
1.0
|
CB
|
B:ASP224
|
4.9
|
54.0
|
1.0
|
C
|
B:ASP220
|
4.9
|
74.8
|
1.0
|
CA
|
B:ASP228
|
5.0
|
69.7
|
1.0
|
O
|
B:TYR261
|
5.0
|
60.4
|
1.0
|
|
Calcium binding site 4 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 4 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca902
b:48.4
occ:1.00
|
OD2
|
B:ASP222
|
2.3
|
66.6
|
1.0
|
OD2
|
B:ASP273
|
2.3
|
55.4
|
1.0
|
O
|
B:GLU263
|
2.3
|
56.4
|
1.0
|
OE2
|
B:GLU231
|
2.3
|
60.5
|
1.0
|
O
|
B:ASN260
|
2.4
|
56.1
|
1.0
|
OD2
|
B:ASP224
|
3.2
|
57.8
|
1.0
|
CD
|
B:GLU231
|
3.4
|
58.7
|
1.0
|
CG
|
B:ASP222
|
3.4
|
69.9
|
1.0
|
CG
|
B:ASP273
|
3.4
|
51.0
|
1.0
|
C
|
B:GLU263
|
3.5
|
60.5
|
1.0
|
C
|
B:ASN260
|
3.5
|
51.8
|
1.0
|
OE1
|
B:GLU231
|
3.8
|
65.8
|
1.0
|
OG1
|
B:THR266
|
4.1
|
44.2
|
1.0
|
CB
|
B:ASP222
|
4.1
|
61.4
|
1.0
|
CB
|
B:ASP273
|
4.2
|
43.2
|
1.0
|
CA
|
B:SER264
|
4.2
|
53.6
|
1.0
|
CG
|
B:ASP224
|
4.2
|
58.6
|
1.0
|
N
|
B:SER264
|
4.3
|
61.8
|
1.0
|
OD1
|
B:ASP273
|
4.3
|
50.2
|
1.0
|
N
|
B:ASN260
|
4.3
|
55.5
|
1.0
|
CA
|
B:TYR261
|
4.4
|
54.5
|
1.0
|
OD1
|
B:ASP222
|
4.4
|
70.4
|
1.0
|
N
|
B:TYR261
|
4.4
|
53.9
|
1.0
|
N
|
B:GLU263
|
4.4
|
59.1
|
1.0
|
OD1
|
B:ASP224
|
4.5
|
63.4
|
1.0
|
CA
|
B:ASN260
|
4.5
|
50.0
|
1.0
|
CB
|
B:SER259
|
4.5
|
48.0
|
1.0
|
C
|
B:SER264
|
4.5
|
51.9
|
1.0
|
CA
|
B:GLU263
|
4.5
|
58.0
|
1.0
|
CG
|
B:GLU231
|
4.6
|
56.8
|
1.0
|
C
|
B:TYR261
|
4.8
|
57.4
|
1.0
|
O
|
B:SER264
|
4.8
|
51.3
|
1.0
|
CA
|
B:CA901
|
4.9
|
70.5
|
1.0
|
CB
|
B:ASN260
|
4.9
|
53.5
|
1.0
|
|
Calcium binding site 5 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 5 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca901
b:63.8
occ:1.00
|
OD1
|
C:ASP222
|
2.2
|
69.6
|
1.0
|
O
|
C:ILE226
|
2.2
|
59.0
|
1.0
|
OE2
|
C:GLU231
|
2.4
|
60.0
|
1.0
|
OD1
|
C:ASP220
|
2.4
|
66.8
|
1.0
|
OD1
|
C:ASP224
|
2.4
|
63.3
|
1.0
|
CG
|
C:ASP222
|
3.0
|
68.2
|
1.0
|
OD2
|
C:ASP222
|
3.1
|
64.7
|
1.0
|
C
|
C:ILE226
|
3.4
|
57.2
|
1.0
|
CG
|
C:ASP224
|
3.5
|
56.6
|
1.0
|
CD
|
C:GLU231
|
3.5
|
54.8
|
1.0
|
CG
|
C:ASP220
|
3.6
|
70.3
|
1.0
|
OD2
|
C:ASP224
|
3.9
|
57.1
|
1.0
|
O
|
C:PRO227
|
4.0
|
63.5
|
1.0
|
C
|
C:PRO227
|
4.1
|
63.2
|
1.0
|
CA
|
C:ILE226
|
4.3
|
54.3
|
1.0
|
N
|
C:PRO227
|
4.3
|
58.8
|
1.0
|
OE1
|
C:GLU231
|
4.3
|
56.4
|
1.0
|
N
|
C:ILE226
|
4.3
|
50.8
|
1.0
|
CA
|
C:PRO227
|
4.4
|
60.8
|
1.0
|
N
|
C:ASP222
|
4.4
|
65.9
|
1.0
|
CG
|
C:GLU231
|
4.4
|
52.4
|
1.0
|
OD1
|
C:ASP228
|
4.4
|
70.8
|
1.0
|
CB
|
C:ASP222
|
4.4
|
59.0
|
1.0
|
N
|
C:THR221
|
4.4
|
64.0
|
1.0
|
OD2
|
C:ASP220
|
4.5
|
72.5
|
1.0
|
CB
|
C:ILE226
|
4.5
|
53.6
|
1.0
|
N
|
C:ASP228
|
4.5
|
68.1
|
1.0
|
N
|
C:ASP224
|
4.5
|
59.2
|
1.0
|
CB
|
C:ASP220
|
4.5
|
70.5
|
1.0
|
CA
|
C:ASP220
|
4.6
|
70.5
|
1.0
|
CA
|
C:CA902
|
4.6
|
44.4
|
1.0
|
N
|
C:ASN223
|
4.7
|
62.0
|
1.0
|
CB
|
C:ASP224
|
4.8
|
47.5
|
1.0
|
O
|
C:TYR261
|
4.8
|
57.2
|
1.0
|
O
|
C:ASP224
|
4.8
|
67.3
|
1.0
|
CA
|
C:ASP222
|
4.8
|
60.8
|
1.0
|
CA
|
C:ASP228
|
4.9
|
63.0
|
1.0
|
C
|
C:ASP224
|
4.9
|
63.8
|
1.0
|
CA
|
C:TYR261
|
4.9
|
54.7
|
1.0
|
C
|
C:ASP220
|
5.0
|
72.2
|
1.0
|
CA
|
C:ASP224
|
5.0
|
54.7
|
1.0
|
|
Calcium binding site 6 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 6 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca902
b:44.4
occ:1.00
|
OD2
|
C:ASP222
|
2.2
|
64.7
|
1.0
|
OD2
|
C:ASP273
|
2.2
|
53.1
|
1.0
|
O
|
C:ASN260
|
2.3
|
55.0
|
1.0
|
O
|
C:GLU263
|
2.4
|
55.4
|
1.0
|
OE1
|
C:GLU231
|
2.5
|
56.4
|
1.0
|
OD2
|
C:ASP224
|
2.9
|
57.1
|
1.0
|
CD
|
C:GLU231
|
3.2
|
54.8
|
1.0
|
OE2
|
C:GLU231
|
3.3
|
60.0
|
1.0
|
CG
|
C:ASP273
|
3.4
|
51.4
|
1.0
|
C
|
C:ASN260
|
3.4
|
49.1
|
1.0
|
CG
|
C:ASP222
|
3.5
|
68.2
|
1.0
|
C
|
C:GLU263
|
3.6
|
61.7
|
1.0
|
CG
|
C:ASP224
|
4.0
|
56.6
|
1.0
|
CB
|
C:ASP273
|
4.1
|
43.7
|
1.0
|
OG1
|
C:THR266
|
4.1
|
44.3
|
1.0
|
N
|
C:ASN260
|
4.2
|
50.8
|
1.0
|
CB
|
C:ASP222
|
4.3
|
59.0
|
1.0
|
CA
|
C:TYR261
|
4.3
|
54.7
|
1.0
|
N
|
C:TYR261
|
4.3
|
52.9
|
1.0
|
OD1
|
C:ASP224
|
4.3
|
63.3
|
1.0
|
CA
|
C:ASN260
|
4.4
|
46.1
|
1.0
|
OD1
|
C:ASP222
|
4.4
|
69.6
|
1.0
|
OD1
|
C:ASP273
|
4.4
|
52.3
|
1.0
|
CB
|
C:SER259
|
4.4
|
47.0
|
1.0
|
CA
|
C:SER264
|
4.4
|
54.2
|
1.0
|
N
|
C:GLU263
|
4.4
|
58.3
|
1.0
|
N
|
C:SER264
|
4.5
|
62.6
|
1.0
|
CA
|
C:GLU263
|
4.6
|
57.9
|
1.0
|
CA
|
C:CA901
|
4.6
|
63.8
|
1.0
|
CG
|
C:GLU231
|
4.7
|
52.4
|
1.0
|
C
|
C:SER264
|
4.7
|
49.9
|
1.0
|
C
|
C:TYR261
|
4.8
|
55.8
|
1.0
|
O
|
C:SER264
|
4.8
|
50.2
|
1.0
|
CB
|
C:ASN260
|
4.8
|
52.0
|
1.0
|
|
Calcium binding site 7 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 7 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca901
b:63.3
occ:1.00
|
OD1
|
D:ASP222
|
2.2
|
72.8
|
1.0
|
O
|
D:ILE226
|
2.2
|
59.6
|
1.0
|
OD1
|
D:ASP220
|
2.3
|
72.6
|
1.0
|
OE2
|
D:GLU231
|
2.4
|
61.9
|
1.0
|
OD1
|
D:ASP224
|
2.4
|
66.6
|
1.0
|
CG
|
D:ASP222
|
3.0
|
72.3
|
1.0
|
OD2
|
D:ASP222
|
3.1
|
69.0
|
1.0
|
CG
|
D:ASP220
|
3.3
|
71.9
|
1.0
|
CG
|
D:ASP224
|
3.4
|
61.0
|
1.0
|
C
|
D:ILE226
|
3.5
|
56.3
|
1.0
|
CD
|
D:GLU231
|
3.5
|
58.5
|
1.0
|
OD2
|
D:ASP220
|
3.7
|
71.5
|
1.0
|
OD2
|
D:ASP224
|
3.7
|
60.1
|
1.0
|
O
|
D:PRO227
|
3.9
|
63.9
|
1.0
|
C
|
D:PRO227
|
4.1
|
64.2
|
1.0
|
OE1
|
D:GLU231
|
4.2
|
58.2
|
1.0
|
CA
|
D:ILE226
|
4.3
|
53.8
|
1.0
|
N
|
D:PRO227
|
4.4
|
59.8
|
1.0
|
N
|
D:ILE226
|
4.4
|
52.1
|
1.0
|
CB
|
D:ASP222
|
4.4
|
63.7
|
1.0
|
N
|
D:ASP222
|
4.4
|
68.6
|
1.0
|
CA
|
D:PRO227
|
4.4
|
62.9
|
1.0
|
CB
|
D:ILE226
|
4.4
|
52.9
|
1.0
|
N
|
D:ASP224
|
4.4
|
63.7
|
1.0
|
CG
|
D:GLU231
|
4.5
|
57.6
|
1.0
|
OD1
|
D:ASP228
|
4.5
|
72.9
|
1.0
|
CA
|
D:CA902
|
4.6
|
44.2
|
1.0
|
N
|
D:THR221
|
4.6
|
66.9
|
1.0
|
CB
|
D:ASP220
|
4.6
|
72.8
|
1.0
|
N
|
D:ASN223
|
4.7
|
64.3
|
1.0
|
CB
|
D:ASP224
|
4.7
|
52.7
|
1.0
|
N
|
D:ASP228
|
4.7
|
70.6
|
1.0
|
CA
|
D:ASP220
|
4.7
|
72.3
|
1.0
|
O
|
D:ASP224
|
4.8
|
70.9
|
1.0
|
O
|
D:TYR261
|
4.8
|
59.5
|
1.0
|
CA
|
D:ASP222
|
4.8
|
64.7
|
1.0
|
C
|
D:ASP224
|
4.9
|
66.5
|
1.0
|
CA
|
D:ASP224
|
4.9
|
60.0
|
1.0
|
CA
|
D:TYR261
|
5.0
|
54.6
|
1.0
|
|
Calcium binding site 8 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 8 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca902
b:44.2
occ:1.00
|
OD2
|
D:ASP222
|
2.3
|
69.0
|
1.0
|
OD2
|
D:ASP273
|
2.3
|
55.2
|
1.0
|
O
|
D:ASN260
|
2.3
|
56.8
|
1.0
|
O
|
D:GLU263
|
2.4
|
55.5
|
1.0
|
OE1
|
D:GLU231
|
2.5
|
58.2
|
1.0
|
OD2
|
D:ASP224
|
3.2
|
60.1
|
1.0
|
CD
|
D:GLU231
|
3.3
|
58.5
|
1.0
|
OE2
|
D:GLU231
|
3.4
|
61.9
|
1.0
|
CG
|
D:ASP273
|
3.4
|
51.3
|
1.0
|
CG
|
D:ASP222
|
3.5
|
72.3
|
1.0
|
C
|
D:ASN260
|
3.5
|
51.8
|
1.0
|
C
|
D:GLU263
|
3.6
|
61.3
|
1.0
|
CB
|
D:ASP273
|
4.1
|
43.8
|
1.0
|
OG1
|
D:THR266
|
4.2
|
42.4
|
1.0
|
CG
|
D:ASP224
|
4.2
|
61.0
|
1.0
|
N
|
D:ASN260
|
4.2
|
56.1
|
1.0
|
CB
|
D:ASP222
|
4.3
|
63.7
|
1.0
|
CA
|
D:TYR261
|
4.3
|
54.6
|
1.0
|
N
|
D:TYR261
|
4.3
|
53.1
|
1.0
|
OD1
|
D:ASP222
|
4.3
|
72.8
|
1.0
|
CA
|
D:SER264
|
4.3
|
53.0
|
1.0
|
OD1
|
D:ASP273
|
4.3
|
49.0
|
1.0
|
CA
|
D:ASN260
|
4.4
|
50.2
|
1.0
|
CB
|
D:SER259
|
4.4
|
46.7
|
1.0
|
N
|
D:SER264
|
4.4
|
62.3
|
1.0
|
OD1
|
D:ASP224
|
4.5
|
66.6
|
1.0
|
N
|
D:GLU263
|
4.5
|
60.1
|
1.0
|
CA
|
D:CA901
|
4.6
|
63.3
|
1.0
|
CA
|
D:GLU263
|
4.6
|
58.5
|
1.0
|
C
|
D:SER264
|
4.6
|
50.3
|
1.0
|
CG
|
D:GLU231
|
4.7
|
57.6
|
1.0
|
O
|
D:SER264
|
4.7
|
51.1
|
1.0
|
C
|
D:TYR261
|
4.7
|
57.2
|
1.0
|
CB
|
D:ASN260
|
4.9
|
55.1
|
1.0
|
|
Calcium binding site 9 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 9 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca901
b:57.2
occ:1.00
|
OD1
|
E:ASP222
|
2.2
|
73.5
|
1.0
|
O
|
E:ILE226
|
2.2
|
59.8
|
1.0
|
OD1
|
E:ASP220
|
2.4
|
71.4
|
1.0
|
OE2
|
E:GLU231
|
2.6
|
59.3
|
1.0
|
OD1
|
E:ASP224
|
2.6
|
63.9
|
1.0
|
CG
|
E:ASP222
|
3.0
|
70.4
|
1.0
|
OD2
|
E:ASP222
|
3.2
|
65.6
|
1.0
|
CG
|
E:ASP220
|
3.4
|
73.5
|
1.0
|
C
|
E:ILE226
|
3.4
|
57.9
|
1.0
|
CD
|
E:GLU231
|
3.6
|
55.8
|
1.0
|
CG
|
E:ASP224
|
3.7
|
60.1
|
1.0
|
O
|
E:PRO227
|
3.8
|
65.4
|
1.0
|
OD2
|
E:ASP220
|
3.9
|
76.3
|
1.0
|
C
|
E:PRO227
|
4.0
|
65.0
|
1.0
|
OD2
|
E:ASP224
|
4.1
|
59.6
|
1.0
|
OD1
|
E:ASP228
|
4.3
|
73.9
|
1.0
|
CA
|
E:PRO227
|
4.3
|
62.7
|
1.0
|
N
|
E:PRO227
|
4.3
|
60.4
|
1.0
|
CA
|
E:ILE226
|
4.3
|
56.6
|
1.0
|
OE1
|
E:GLU231
|
4.4
|
56.3
|
1.0
|
CG
|
E:GLU231
|
4.4
|
54.7
|
1.0
|
N
|
E:ASP222
|
4.4
|
68.4
|
1.0
|
CB
|
E:ASP222
|
4.5
|
60.1
|
1.0
|
CB
|
E:ILE226
|
4.5
|
55.5
|
1.0
|
N
|
E:THR221
|
4.5
|
67.2
|
1.0
|
N
|
E:ILE226
|
4.5
|
50.7
|
1.0
|
N
|
E:ASP228
|
4.5
|
69.3
|
1.0
|
CA
|
E:ASP220
|
4.6
|
71.3
|
1.0
|
CB
|
E:ASP220
|
4.6
|
73.8
|
1.0
|
CA
|
E:CA902
|
4.6
|
44.8
|
1.0
|
N
|
E:ASP224
|
4.6
|
61.7
|
1.0
|
O
|
E:TYR261
|
4.7
|
58.7
|
1.0
|
N
|
E:ASN223
|
4.8
|
63.3
|
1.0
|
O
|
E:ASP224
|
4.8
|
70.1
|
1.0
|
CA
|
E:TYR261
|
4.8
|
52.4
|
1.0
|
CA
|
E:ASP228
|
4.9
|
65.9
|
1.0
|
CA
|
E:ASP222
|
4.9
|
62.3
|
1.0
|
CB
|
E:ASP224
|
5.0
|
53.5
|
1.0
|
|
Calcium binding site 10 out
of 14 in 8ekl
Go back to
Calcium Binding Sites List in 8ekl
Calcium binding site 10 out
of 14 in the Clostridioides Difficile Binary Toxin Translocase Cdtb Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1
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 Wild-Type After Calcium Depletion From Receptor Binding Domain 1 (RBD1) - Class 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca902
b:44.8
occ:1.00
|
OD2
|
E:ASP222
|
2.3
|
65.6
|
1.0
|
OD2
|
E:ASP273
|
2.3
|
55.5
|
1.0
|
O
|
E:ASN260
|
2.3
|
56.6
|
1.0
|
O
|
E:GLU263
|
2.4
|
54.0
|
1.0
|
OE1
|
E:GLU231
|
2.6
|
56.3
|
1.0
|
OE2
|
E:GLU231
|
3.2
|
59.3
|
1.0
|
OD2
|
E:ASP224
|
3.2
|
59.6
|
1.0
|
CD
|
E:GLU231
|
3.3
|
55.8
|
1.0
|
C
|
E:ASN260
|
3.4
|
50.0
|
1.0
|
CG
|
E:ASP273
|
3.4
|
52.5
|
1.0
|
CG
|
E:ASP222
|
3.4
|
70.4
|
1.0
|
C
|
E:GLU263
|
3.6
|
60.1
|
1.0
|
CB
|
E:ASP273
|
4.1
|
44.9
|
1.0
|
CG
|
E:ASP224
|
4.2
|
60.1
|
1.0
|
OG1
|
E:THR266
|
4.2
|
41.5
|
1.0
|
CA
|
E:TYR261
|
4.2
|
52.4
|
1.0
|
N
|
E:ASN260
|
4.2
|
53.1
|
1.0
|
CB
|
E:ASP222
|
4.2
|
60.1
|
1.0
|
N
|
E:TYR261
|
4.3
|
50.7
|
1.0
|
OD1
|
E:ASP222
|
4.3
|
73.5
|
1.0
|
CA
|
E:SER264
|
4.4
|
50.6
|
1.0
|
OD1
|
E:ASP273
|
4.4
|
51.0
|
1.0
|
CB
|
E:SER259
|
4.4
|
48.2
|
1.0
|
CA
|
E:ASN260
|
4.4
|
48.2
|
1.0
|
OD1
|
E:ASP224
|
4.4
|
63.9
|
1.0
|
N
|
E:GLU263
|
4.5
|
58.1
|
1.0
|
N
|
E:SER264
|
4.5
|
60.1
|
1.0
|
CA
|
E:CA901
|
4.6
|
57.2
|
1.0
|
CA
|
E:GLU263
|
4.6
|
57.8
|
1.0
|
C
|
E:SER264
|
4.7
|
48.6
|
1.0
|
C
|
E:TYR261
|
4.7
|
55.1
|
1.0
|
CG
|
E:GLU231
|
4.7
|
54.7
|
1.0
|
O
|
E:SER264
|
4.8
|
50.9
|
1.0
|
CB
|
E:ASN260
|
4.9
|
53.8
|
1.0
|
|
Reference:
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.
Page generated: Fri Jul 19 08:14:40 2024
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