Calcium in PDB 7vnj: Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
21;
Binding sites:
The binding sites of Calcium atom in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
(pdb code 7vnj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 21 binding sites of Calcium where determined in the
Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem, PDB code: 7vnj:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 21 in 7vnj
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Calcium Binding Sites List in 7vnj
Calcium binding site 1 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca901
b:52.0
occ:1.00
|
OD2
|
A:ASP224
|
2.3
|
57.4
|
1.0
|
O
|
A:ASN260
|
2.4
|
54.3
|
1.0
|
O
|
A:GLU263
|
2.4
|
54.9
|
1.0
|
OD2
|
A:ASP273
|
2.4
|
51.7
|
1.0
|
OD2
|
A:ASP222
|
2.4
|
57.4
|
1.0
|
OE1
|
A:GLU231
|
2.6
|
55.3
|
1.0
|
OE2
|
A:GLU231
|
3.0
|
55.3
|
1.0
|
CD
|
A:GLU231
|
3.2
|
55.3
|
1.0
|
CG
|
A:ASP224
|
3.5
|
57.4
|
1.0
|
CG
|
A:ASP273
|
3.5
|
51.7
|
1.0
|
C
|
A:GLU263
|
3.5
|
54.9
|
1.0
|
C
|
A:ASN260
|
3.5
|
54.3
|
1.0
|
CG
|
A:ASP222
|
3.6
|
57.4
|
1.0
|
CB
|
A:ASP273
|
4.1
|
51.7
|
1.0
|
OG
|
A:SER259
|
4.1
|
52.9
|
1.0
|
CA
|
A:SER264
|
4.2
|
53.8
|
1.0
|
OD1
|
A:ASP224
|
4.2
|
57.4
|
1.0
|
OG1
|
A:THR266
|
4.2
|
50.9
|
1.0
|
OD1
|
A:ASP222
|
4.2
|
57.4
|
1.0
|
CA
|
A:TYR261
|
4.2
|
56.4
|
1.0
|
N
|
A:SER264
|
4.3
|
53.8
|
1.0
|
N
|
A:TYR261
|
4.3
|
56.4
|
1.0
|
N
|
A:GLU263
|
4.4
|
54.9
|
1.0
|
O
|
A:SER264
|
4.4
|
53.8
|
1.0
|
C
|
A:SER264
|
4.4
|
53.8
|
1.0
|
N
|
A:ASN260
|
4.4
|
54.3
|
1.0
|
OD1
|
A:ASP273
|
4.5
|
51.7
|
1.0
|
CA
|
A:CA902
|
4.5
|
54.5
|
1.0
|
CA
|
A:ASN260
|
4.5
|
54.3
|
1.0
|
CB
|
A:ASP224
|
4.5
|
57.4
|
1.0
|
CA
|
A:GLU263
|
4.5
|
54.9
|
1.0
|
C
|
A:TYR261
|
4.6
|
56.4
|
1.0
|
CG
|
A:GLU231
|
4.6
|
55.3
|
1.0
|
CB
|
A:ASP222
|
4.7
|
57.4
|
1.0
|
CB
|
A:SER259
|
4.8
|
52.9
|
1.0
|
O
|
A:TYR261
|
4.9
|
56.4
|
1.0
|
CB
|
A:ASN260
|
4.9
|
54.3
|
1.0
|
|
Calcium binding site 2 out
of 21 in 7vnj
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Calcium Binding Sites List in 7vnj
Calcium binding site 2 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca902
b:54.5
occ:1.00
|
O
|
A:ILE226
|
2.3
|
57.1
|
1.0
|
OD1
|
A:ASP222
|
2.3
|
57.4
|
1.0
|
OE2
|
A:GLU231
|
2.4
|
55.3
|
1.0
|
OD1
|
A:ASP220
|
2.4
|
59.9
|
1.0
|
OD1
|
A:ASP224
|
2.5
|
57.4
|
1.0
|
CG
|
A:ASP222
|
3.2
|
57.4
|
1.0
|
CG
|
A:ASP224
|
3.4
|
57.4
|
1.0
|
OD2
|
A:ASP222
|
3.5
|
57.4
|
1.0
|
C
|
A:ILE226
|
3.5
|
57.1
|
1.0
|
CD
|
A:GLU231
|
3.5
|
55.3
|
1.0
|
CG
|
A:ASP220
|
3.5
|
59.9
|
1.0
|
OD1
|
A:ASP228
|
3.6
|
58.8
|
1.0
|
OD2
|
A:ASP224
|
3.7
|
57.4
|
1.0
|
O
|
A:TYR261
|
4.1
|
56.4
|
1.0
|
CG
|
A:GLU231
|
4.2
|
55.3
|
1.0
|
C
|
A:PRO227
|
4.2
|
58.7
|
1.0
|
OD2
|
A:ASP220
|
4.3
|
59.9
|
1.0
|
CA
|
A:ILE226
|
4.3
|
57.1
|
1.0
|
N
|
A:ILE226
|
4.3
|
57.1
|
1.0
|
CA
|
A:ASP220
|
4.3
|
59.9
|
1.0
|
O
|
A:PRO227
|
4.4
|
58.7
|
1.0
|
CB
|
A:ILE226
|
4.4
|
57.1
|
1.0
|
N
|
A:ASP222
|
4.4
|
57.4
|
1.0
|
N
|
A:ASP228
|
4.4
|
58.8
|
1.0
|
N
|
A:ASP224
|
4.5
|
57.4
|
1.0
|
CA
|
A:CA901
|
4.5
|
52.0
|
1.0
|
N
|
A:PRO227
|
4.5
|
58.7
|
1.0
|
N
|
A:THR221
|
4.5
|
58.8
|
1.0
|
CB
|
A:ASP220
|
4.5
|
59.9
|
1.0
|
OE1
|
A:GLU231
|
4.5
|
55.3
|
1.0
|
CA
|
A:PRO227
|
4.6
|
58.7
|
1.0
|
CB
|
A:ASP222
|
4.6
|
57.4
|
1.0
|
CA
|
A:TYR261
|
4.6
|
56.4
|
1.0
|
C
|
A:ASP220
|
4.6
|
59.9
|
1.0
|
N
|
A:ASN223
|
4.7
|
59.4
|
1.0
|
CB
|
A:ASP224
|
4.7
|
57.4
|
1.0
|
CA
|
A:ASP228
|
4.7
|
58.8
|
1.0
|
C
|
A:TYR261
|
4.8
|
56.4
|
1.0
|
CG
|
A:ASP228
|
4.8
|
58.8
|
1.0
|
CB
|
A:TYR261
|
4.9
|
56.4
|
1.0
|
CA
|
A:ASP222
|
4.9
|
57.4
|
1.0
|
|
Calcium binding site 3 out
of 21 in 7vnj
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Calcium Binding Sites List in 7vnj
Calcium binding site 3 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca903
b:127.2
occ:1.00
|
OG
|
A:SER646
|
2.4
|
141.7
|
1.0
|
OD2
|
A:ASP734
|
2.4
|
127.4
|
1.0
|
OD1
|
A:ASP734
|
2.5
|
127.4
|
1.0
|
O
|
A:ASN621
|
2.5
|
123.2
|
1.0
|
OD2
|
A:ASP623
|
2.5
|
127.1
|
1.0
|
CG
|
A:ASP734
|
2.8
|
127.4
|
1.0
|
CG
|
A:ASP623
|
3.4
|
127.1
|
1.0
|
C
|
A:ASN621
|
3.6
|
123.2
|
1.0
|
CB
|
A:SER646
|
3.7
|
141.7
|
1.0
|
OD1
|
A:ASP623
|
3.8
|
127.1
|
1.0
|
N
|
A:GLN644
|
3.8
|
130.2
|
1.0
|
CB
|
A:ASN621
|
3.8
|
123.2
|
1.0
|
C
|
A:GLN644
|
3.9
|
130.2
|
1.0
|
CB
|
A:GLN644
|
4.0
|
130.2
|
1.0
|
CA
|
A:ASN621
|
4.0
|
123.2
|
1.0
|
N
|
A:SER646
|
4.0
|
141.7
|
1.0
|
CA
|
A:GLN644
|
4.1
|
130.2
|
1.0
|
N
|
A:GLY645
|
4.1
|
134.4
|
1.0
|
OD1
|
A:ASN735
|
4.2
|
119.4
|
1.0
|
O
|
A:GLN644
|
4.2
|
130.2
|
1.0
|
CB
|
A:ASP734
|
4.3
|
127.4
|
1.0
|
CA
|
A:SER646
|
4.4
|
141.7
|
1.0
|
OE1
|
A:GLN644
|
4.4
|
130.2
|
1.0
|
C
|
A:GLY645
|
4.5
|
134.4
|
1.0
|
O
|
A:SER646
|
4.5
|
141.7
|
1.0
|
CB
|
A:ASP623
|
4.6
|
127.1
|
1.0
|
N
|
A:PHE622
|
4.7
|
130.9
|
1.0
|
N
|
A:LEU643
|
4.8
|
128.3
|
1.0
|
C
|
A:SER646
|
4.8
|
141.7
|
1.0
|
CA
|
A:GLY645
|
4.9
|
134.4
|
1.0
|
CG
|
A:ASN621
|
4.9
|
123.2
|
1.0
|
N
|
A:ASP623
|
4.9
|
127.1
|
1.0
|
CG
|
A:ASN735
|
4.9
|
119.4
|
1.0
|
C
|
A:LEU643
|
4.9
|
128.3
|
1.0
|
|
Calcium binding site 4 out
of 21 in 7vnj
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Calcium Binding Sites List in 7vnj
Calcium binding site 4 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca901
b:49.7
occ:1.00
|
O
|
B:GLU263
|
2.4
|
53.7
|
1.0
|
O
|
B:ASN260
|
2.4
|
53.0
|
1.0
|
OD2
|
B:ASP224
|
2.4
|
55.7
|
1.0
|
OD2
|
B:ASP273
|
2.5
|
50.8
|
1.0
|
OD2
|
B:ASP222
|
2.6
|
56.2
|
1.0
|
OE1
|
B:GLU231
|
2.7
|
53.7
|
1.0
|
OE2
|
B:GLU231
|
2.9
|
53.7
|
1.0
|
CD
|
B:GLU231
|
3.2
|
53.7
|
1.0
|
CG
|
B:ASP224
|
3.4
|
55.7
|
1.0
|
C
|
B:GLU263
|
3.5
|
53.7
|
1.0
|
C
|
B:ASN260
|
3.6
|
53.0
|
1.0
|
CG
|
B:ASP273
|
3.6
|
50.8
|
1.0
|
CG
|
B:ASP222
|
3.7
|
56.2
|
1.0
|
OD1
|
B:ASP224
|
4.0
|
55.7
|
1.0
|
OG1
|
B:THR266
|
4.2
|
49.5
|
1.0
|
CB
|
B:ASP273
|
4.2
|
50.8
|
1.0
|
OD1
|
B:ASP222
|
4.2
|
56.2
|
1.0
|
CA
|
B:TYR261
|
4.2
|
54.6
|
1.0
|
CA
|
B:SER264
|
4.2
|
52.1
|
1.0
|
N
|
B:SER264
|
4.3
|
52.1
|
1.0
|
N
|
B:TYR261
|
4.3
|
54.6
|
1.0
|
CA
|
B:CA902
|
4.3
|
53.4
|
1.0
|
N
|
B:GLU263
|
4.3
|
53.7
|
1.0
|
CB
|
B:ASP224
|
4.4
|
55.7
|
1.0
|
O
|
B:SER264
|
4.4
|
52.1
|
1.0
|
OG
|
B:SER259
|
4.5
|
51.0
|
1.0
|
OD1
|
B:ASP273
|
4.5
|
50.8
|
1.0
|
C
|
B:SER264
|
4.5
|
52.1
|
1.0
|
CA
|
B:GLU263
|
4.5
|
53.7
|
1.0
|
N
|
B:ASN260
|
4.6
|
53.0
|
1.0
|
C
|
B:TYR261
|
4.6
|
54.6
|
1.0
|
CA
|
B:ASN260
|
4.6
|
53.0
|
1.0
|
CG
|
B:GLU231
|
4.7
|
53.7
|
1.0
|
CB
|
B:SER259
|
4.8
|
51.0
|
1.0
|
CB
|
B:ASP222
|
4.8
|
56.2
|
1.0
|
O
|
B:TYR261
|
5.0
|
54.6
|
1.0
|
N
|
B:LEU262
|
5.0
|
54.3
|
1.0
|
|
Calcium binding site 5 out
of 21 in 7vnj
Go back to
Calcium Binding Sites List in 7vnj
Calcium binding site 5 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca902
b:53.4
occ:1.00
|
O
|
B:ILE226
|
2.3
|
55.8
|
1.0
|
OD1
|
B:ASP222
|
2.3
|
56.2
|
1.0
|
OE2
|
B:GLU231
|
2.4
|
53.7
|
1.0
|
OD1
|
B:ASP224
|
2.4
|
55.7
|
1.0
|
OD1
|
B:ASP220
|
2.4
|
59.3
|
1.0
|
CG
|
B:ASP222
|
3.3
|
56.2
|
1.0
|
CG
|
B:ASP224
|
3.4
|
55.7
|
1.0
|
C
|
B:ILE226
|
3.5
|
55.8
|
1.0
|
OD2
|
B:ASP222
|
3.5
|
56.2
|
1.0
|
CG
|
B:ASP220
|
3.6
|
59.3
|
1.0
|
CD
|
B:GLU231
|
3.6
|
53.7
|
1.0
|
OD1
|
B:ASP228
|
3.6
|
57.7
|
1.0
|
OD2
|
B:ASP224
|
3.7
|
55.7
|
1.0
|
N
|
B:ILE226
|
4.2
|
55.8
|
1.0
|
CG
|
B:GLU231
|
4.2
|
53.7
|
1.0
|
O
|
B:TYR261
|
4.2
|
54.6
|
1.0
|
OD2
|
B:ASP220
|
4.3
|
59.3
|
1.0
|
CA
|
B:ILE226
|
4.3
|
55.8
|
1.0
|
CA
|
B:ASP220
|
4.3
|
59.3
|
1.0
|
CA
|
B:CA901
|
4.3
|
49.7
|
1.0
|
C
|
B:PRO227
|
4.3
|
57.2
|
1.0
|
N
|
B:ASP222
|
4.4
|
56.2
|
1.0
|
CB
|
B:ILE226
|
4.5
|
55.8
|
1.0
|
N
|
B:ASP224
|
4.5
|
55.7
|
1.0
|
N
|
B:ASP228
|
4.5
|
57.7
|
1.0
|
N
|
B:PRO227
|
4.5
|
57.2
|
1.0
|
N
|
B:THR221
|
4.5
|
57.4
|
1.0
|
O
|
B:PRO227
|
4.5
|
57.2
|
1.0
|
OE1
|
B:GLU231
|
4.5
|
53.7
|
1.0
|
CB
|
B:ASP220
|
4.6
|
59.3
|
1.0
|
CA
|
B:TYR261
|
4.6
|
54.6
|
1.0
|
CA
|
B:PRO227
|
4.6
|
57.2
|
1.0
|
CB
|
B:ASP224
|
4.6
|
55.7
|
1.0
|
CB
|
B:ASP222
|
4.7
|
56.2
|
1.0
|
C
|
B:ASP220
|
4.7
|
59.3
|
1.0
|
N
|
B:ASN223
|
4.8
|
57.7
|
1.0
|
C
|
B:TYR261
|
4.8
|
54.6
|
1.0
|
CA
|
B:ASP228
|
4.8
|
57.7
|
1.0
|
CG
|
B:ASP228
|
4.8
|
57.7
|
1.0
|
CB
|
B:TYR261
|
4.9
|
54.6
|
1.0
|
CA
|
B:ASP222
|
4.9
|
56.2
|
1.0
|
CA
|
B:ASP224
|
5.0
|
55.7
|
1.0
|
|
Calcium binding site 6 out
of 21 in 7vnj
Go back to
Calcium Binding Sites List in 7vnj
Calcium binding site 6 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca903
b:125.4
occ:1.00
|
OG
|
B:SER646
|
2.4
|
139.6
|
1.0
|
OD2
|
B:ASP734
|
2.5
|
128.3
|
1.0
|
O
|
B:ASN621
|
2.5
|
125.9
|
1.0
|
OD1
|
B:ASP734
|
2.6
|
128.3
|
1.0
|
OD1
|
B:ASP623
|
2.7
|
130.5
|
1.0
|
CG
|
B:ASP734
|
2.9
|
128.3
|
1.0
|
O
|
B:GLN644
|
3.0
|
132.1
|
1.0
|
O
|
B:SER646
|
3.2
|
139.6
|
1.0
|
C
|
B:GLN644
|
3.6
|
132.1
|
1.0
|
N
|
B:GLN644
|
3.6
|
132.1
|
1.0
|
C
|
B:ASN621
|
3.7
|
125.9
|
1.0
|
CB
|
B:SER646
|
3.7
|
139.6
|
1.0
|
N
|
B:SER646
|
3.8
|
139.6
|
1.0
|
CG
|
B:ASP623
|
3.9
|
130.5
|
1.0
|
C
|
B:SER646
|
4.0
|
139.6
|
1.0
|
CA
|
B:SER646
|
4.0
|
139.6
|
1.0
|
CA
|
B:GLN644
|
4.0
|
132.1
|
1.0
|
OD1
|
B:ASN735
|
4.1
|
121.0
|
1.0
|
CB
|
B:ASN621
|
4.1
|
125.9
|
1.0
|
CA
|
B:ASN621
|
4.2
|
125.9
|
1.0
|
CB
|
B:GLN644
|
4.3
|
132.1
|
1.0
|
CB
|
B:ASP734
|
4.4
|
128.3
|
1.0
|
OD2
|
B:ASP623
|
4.4
|
130.5
|
1.0
|
N
|
B:GLY645
|
4.5
|
135.8
|
1.0
|
N
|
B:LEU643
|
4.5
|
130.0
|
1.0
|
C
|
B:GLY645
|
4.6
|
135.8
|
1.0
|
N
|
B:PHE622
|
4.8
|
129.9
|
1.0
|
C
|
B:LEU643
|
4.8
|
130.0
|
1.0
|
CB
|
B:PHE622
|
4.9
|
129.9
|
1.0
|
OE1
|
B:GLN644
|
4.9
|
132.1
|
1.0
|
O
|
B:ASP641
|
4.9
|
147.6
|
1.0
|
CA
|
B:GLY642
|
5.0
|
138.5
|
1.0
|
C
|
B:GLY642
|
5.0
|
138.5
|
1.0
|
|
Calcium binding site 7 out
of 21 in 7vnj
Go back to
Calcium Binding Sites List in 7vnj
Calcium binding site 7 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca901
b:48.6
occ:1.00
|
O
|
C:ASN260
|
2.4
|
51.3
|
1.0
|
OD2
|
C:ASP273
|
2.4
|
50.2
|
1.0
|
OD2
|
C:ASP222
|
2.4
|
53.8
|
1.0
|
O
|
C:GLU263
|
2.5
|
52.2
|
1.0
|
OE1
|
C:GLU231
|
2.5
|
51.7
|
1.0
|
OD2
|
C:ASP224
|
2.5
|
54.0
|
1.0
|
OE2
|
C:GLU231
|
3.0
|
51.7
|
1.0
|
CD
|
C:GLU231
|
3.1
|
51.7
|
1.0
|
C
|
C:ASN260
|
3.5
|
51.3
|
1.0
|
CG
|
C:ASP224
|
3.5
|
54.0
|
1.0
|
CG
|
C:ASP273
|
3.6
|
50.2
|
1.0
|
C
|
C:GLU263
|
3.6
|
52.2
|
1.0
|
CG
|
C:ASP222
|
3.6
|
53.8
|
1.0
|
OG1
|
C:THR266
|
4.1
|
48.7
|
1.0
|
CA
|
C:SER264
|
4.1
|
50.6
|
1.0
|
CB
|
C:ASP273
|
4.2
|
50.2
|
1.0
|
OD1
|
C:ASP224
|
4.2
|
54.0
|
1.0
|
CA
|
C:TYR261
|
4.2
|
52.6
|
1.0
|
OD1
|
C:ASP222
|
4.2
|
53.8
|
1.0
|
OG
|
C:SER259
|
4.2
|
50.0
|
1.0
|
O
|
C:SER264
|
4.3
|
50.6
|
1.0
|
N
|
C:SER264
|
4.3
|
50.6
|
1.0
|
N
|
C:TYR261
|
4.3
|
52.6
|
1.0
|
C
|
C:SER264
|
4.4
|
50.6
|
1.0
|
CA
|
C:CA902
|
4.4
|
52.7
|
1.0
|
N
|
C:GLU263
|
4.5
|
52.2
|
1.0
|
N
|
C:ASN260
|
4.5
|
51.3
|
1.0
|
CB
|
C:ASP224
|
4.5
|
54.0
|
1.0
|
CA
|
C:ASN260
|
4.6
|
51.3
|
1.0
|
C
|
C:TYR261
|
4.6
|
52.6
|
1.0
|
OD1
|
C:ASP273
|
4.6
|
50.2
|
1.0
|
CG
|
C:GLU231
|
4.6
|
51.7
|
1.0
|
CA
|
C:GLU263
|
4.7
|
52.2
|
1.0
|
CB
|
C:ASP222
|
4.7
|
53.8
|
1.0
|
CB
|
C:SER259
|
4.7
|
50.0
|
1.0
|
O
|
C:TYR261
|
4.9
|
52.6
|
1.0
|
|
Calcium binding site 8 out
of 21 in 7vnj
Go back to
Calcium Binding Sites List in 7vnj
Calcium binding site 8 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca902
b:52.7
occ:1.00
|
OD1
|
C:ASP222
|
2.3
|
53.8
|
1.0
|
O
|
C:ILE226
|
2.3
|
54.4
|
1.0
|
OE2
|
C:GLU231
|
2.4
|
51.7
|
1.0
|
OD1
|
C:ASP224
|
2.4
|
54.0
|
1.0
|
OD1
|
C:ASP220
|
2.4
|
58.4
|
1.0
|
CG
|
C:ASP222
|
3.3
|
53.8
|
1.0
|
CG
|
C:ASP224
|
3.3
|
54.0
|
1.0
|
C
|
C:ILE226
|
3.5
|
54.4
|
1.0
|
OD2
|
C:ASP222
|
3.5
|
53.8
|
1.0
|
CD
|
C:GLU231
|
3.5
|
51.7
|
1.0
|
OD1
|
C:ASP228
|
3.6
|
55.9
|
1.0
|
OD2
|
C:ASP224
|
3.7
|
54.0
|
1.0
|
CG
|
C:ASP220
|
3.7
|
58.4
|
1.0
|
N
|
C:ILE226
|
4.1
|
54.4
|
1.0
|
CA
|
C:ILE226
|
4.2
|
54.4
|
1.0
|
O
|
C:TYR261
|
4.2
|
52.6
|
1.0
|
CG
|
C:GLU231
|
4.2
|
51.7
|
1.0
|
CB
|
C:ILE226
|
4.3
|
54.4
|
1.0
|
CA
|
C:ASP220
|
4.4
|
58.4
|
1.0
|
C
|
C:PRO227
|
4.4
|
55.5
|
1.0
|
N
|
C:ASP222
|
4.4
|
53.8
|
1.0
|
OD2
|
C:ASP220
|
4.4
|
58.4
|
1.0
|
CA
|
C:CA901
|
4.4
|
48.6
|
1.0
|
N
|
C:ASP224
|
4.5
|
54.0
|
1.0
|
OE1
|
C:GLU231
|
4.5
|
51.7
|
1.0
|
N
|
C:THR221
|
4.5
|
55.3
|
1.0
|
O
|
C:PRO227
|
4.5
|
55.5
|
1.0
|
N
|
C:ASP228
|
4.6
|
55.9
|
1.0
|
N
|
C:PRO227
|
4.6
|
55.5
|
1.0
|
CB
|
C:ASP220
|
4.6
|
58.4
|
1.0
|
CB
|
C:ASP224
|
4.6
|
54.0
|
1.0
|
CB
|
C:ASP222
|
4.6
|
53.8
|
1.0
|
CA
|
C:TYR261
|
4.7
|
52.6
|
1.0
|
C
|
C:ASP220
|
4.7
|
58.4
|
1.0
|
CA
|
C:PRO227
|
4.7
|
55.5
|
1.0
|
N
|
C:ASN223
|
4.8
|
54.9
|
1.0
|
CG
|
C:ASP228
|
4.8
|
55.9
|
1.0
|
CA
|
C:ASP228
|
4.8
|
55.9
|
1.0
|
C
|
C:TYR261
|
4.9
|
52.6
|
1.0
|
CA
|
C:ASP222
|
4.9
|
53.8
|
1.0
|
CA
|
C:ASP224
|
4.9
|
54.0
|
1.0
|
CB
|
C:TYR261
|
5.0
|
52.6
|
1.0
|
|
Calcium binding site 9 out
of 21 in 7vnj
Go back to
Calcium Binding Sites List in 7vnj
Calcium binding site 9 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca903
b:121.8
occ:1.00
|
OG
|
C:SER646
|
2.3
|
137.4
|
1.0
|
O
|
C:ASN621
|
2.5
|
123.0
|
1.0
|
OD2
|
C:ASP623
|
2.6
|
127.0
|
1.0
|
OD1
|
C:ASP734
|
2.7
|
126.5
|
1.0
|
OD2
|
C:ASP734
|
2.7
|
126.5
|
1.0
|
CG
|
C:ASP734
|
3.1
|
126.5
|
1.0
|
CB
|
C:SER646
|
3.5
|
137.4
|
1.0
|
C
|
C:ASN621
|
3.6
|
123.0
|
1.0
|
CG
|
C:ASP623
|
3.6
|
127.0
|
1.0
|
CB
|
C:ASN621
|
3.7
|
123.0
|
1.0
|
N
|
C:GLN644
|
3.9
|
126.8
|
1.0
|
CA
|
C:ASN621
|
3.9
|
123.0
|
1.0
|
OD1
|
C:ASP623
|
4.1
|
127.0
|
1.0
|
OD1
|
C:ASN735
|
4.1
|
118.6
|
1.0
|
CB
|
C:GLN644
|
4.1
|
126.8
|
1.0
|
OE1
|
C:GLN644
|
4.2
|
126.8
|
1.0
|
C
|
C:GLN644
|
4.2
|
126.8
|
1.0
|
CA
|
C:GLN644
|
4.3
|
126.8
|
1.0
|
N
|
C:SER646
|
4.3
|
137.4
|
1.0
|
O
|
C:GLN644
|
4.4
|
126.8
|
1.0
|
CA
|
C:SER646
|
4.5
|
137.4
|
1.0
|
N
|
C:GLY645
|
4.5
|
131.8
|
1.0
|
CB
|
C:ASP734
|
4.6
|
126.5
|
1.0
|
O
|
C:SER646
|
4.7
|
137.4
|
1.0
|
C
|
C:GLY645
|
4.7
|
131.8
|
1.0
|
CB
|
C:ASP623
|
4.7
|
127.0
|
1.0
|
N
|
C:PHE622
|
4.8
|
127.7
|
1.0
|
CG
|
C:ASN621
|
4.8
|
123.0
|
1.0
|
N
|
C:LEU643
|
4.9
|
124.4
|
1.0
|
CG
|
C:ASN735
|
4.9
|
118.6
|
1.0
|
N
|
C:ASP623
|
5.0
|
127.0
|
1.0
|
|
Calcium binding site 10 out
of 21 in 7vnj
Go back to
Calcium Binding Sites List in 7vnj
Calcium binding site 10 out
of 21 in the Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Complex Structure of Clostridioides Difficile Enzymatic Component (Cdta) and Binding Component (Cdtb) Pore with Short Stem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca901
b:48.3
occ:1.00
|
O
|
D:GLU263
|
2.4
|
51.0
|
1.0
|
OD2
|
D:ASP222
|
2.4
|
53.8
|
1.0
|
OD2
|
D:ASP273
|
2.4
|
49.1
|
1.0
|
OE1
|
D:GLU231
|
2.4
|
50.9
|
1.0
|
O
|
D:ASN260
|
2.5
|
50.9
|
1.0
|
OD2
|
D:ASP224
|
2.5
|
52.5
|
1.0
|
OE2
|
D:GLU231
|
3.1
|
50.9
|
1.0
|
CD
|
D:GLU231
|
3.2
|
50.9
|
1.0
|
CG
|
D:ASP273
|
3.5
|
49.1
|
1.0
|
CG
|
D:ASP224
|
3.5
|
52.5
|
1.0
|
C
|
D:GLU263
|
3.5
|
51.0
|
1.0
|
CG
|
D:ASP222
|
3.6
|
53.8
|
1.0
|
C
|
D:ASN260
|
3.6
|
50.9
|
1.0
|
OD1
|
D:ASP224
|
4.1
|
52.5
|
1.0
|
CB
|
D:ASP273
|
4.1
|
49.1
|
1.0
|
CA
|
D:SER264
|
4.1
|
48.7
|
1.0
|
OG
|
D:SER259
|
4.2
|
49.6
|
1.0
|
OG1
|
D:THR266
|
4.2
|
47.5
|
1.0
|
O
|
D:SER264
|
4.2
|
48.7
|
1.0
|
OD1
|
D:ASP222
|
4.3
|
53.8
|
1.0
|
N
|
D:SER264
|
4.3
|
48.7
|
1.0
|
CA
|
D:TYR261
|
4.3
|
51.6
|
1.0
|
C
|
D:SER264
|
4.4
|
48.7
|
1.0
|
N
|
D:GLU263
|
4.4
|
51.0
|
1.0
|
N
|
D:TYR261
|
4.4
|
51.6
|
1.0
|
CA
|
D:CA902
|
4.4
|
51.1
|
1.0
|
OD1
|
D:ASP273
|
4.5
|
49.1
|
1.0
|
CA
|
D:GLU263
|
4.6
|
51.0
|
1.0
|
CB
|
D:ASP224
|
4.6
|
52.5
|
1.0
|
N
|
D:ASN260
|
4.6
|
50.9
|
1.0
|
CG
|
D:GLU231
|
4.6
|
50.9
|
1.0
|
CA
|
D:ASN260
|
4.6
|
50.9
|
1.0
|
C
|
D:TYR261
|
4.7
|
51.6
|
1.0
|
CB
|
D:ASP222
|
4.7
|
53.8
|
1.0
|
CB
|
D:SER259
|
4.8
|
49.6
|
1.0
|
O
|
D:TYR261
|
4.9
|
51.6
|
1.0
|
|
Reference:
A.Kawamoto,
T.Yamada,
T.Yoshida,
Y.Sato,
T.Kato,
H.Tsuge.
Cryo-Em Structures of the Translocational Binary Toxin Complex Cdta-Bound Cdtb-Pore From Clostridioides Difficile. Nat Commun V. 13 6119 2022.
ISSN: ESSN 2041-1723
PubMed: 36253419
DOI: 10.1038/S41467-022-33888-4
Page generated: Fri Jul 19 05:22:38 2024
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