Calcium in PDB 4wb2: Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
Protein crystallography data
The structure of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin, PDB code: 4wb2
was solved by
L.Yatime,
C.Maasch,
K.Hoehlig,
S.Klussmann,
A.Vater,
G.R.Andersen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.88 /
1.80
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.470,
282.254,
45.899,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.7 /
19.3
|
Other elements in 4wb2:
The structure of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
(pdb code 4wb2). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin, PDB code: 4wb2:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 4wb2
Go back to
Calcium Binding Sites List in 4wb2
Calcium binding site 1 out
of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_01.jpg) Mono view
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca802
b:15.9
occ:1.00
|
OP2
|
D:0G32
|
2.3
|
16.4
|
1.0
|
OP2
|
D:0U5
|
2.3
|
18.2
|
1.0
|
O
|
D:HOH256
|
2.5
|
19.8
|
1.0
|
OP1
|
D:0G6
|
2.5
|
13.9
|
1.0
|
OD2
|
A:ASP705
|
2.5
|
17.8
|
1.0
|
O
|
D:HOH247
|
2.5
|
12.8
|
1.0
|
O
|
D:HOH248
|
2.6
|
15.5
|
1.0
|
CG
|
A:ASP705
|
3.4
|
19.4
|
1.0
|
P
|
D:0U5
|
3.6
|
18.1
|
1.0
|
P
|
D:0G6
|
3.7
|
16.4
|
1.0
|
P
|
D:0G32
|
3.7
|
15.9
|
1.0
|
O
|
D:HOH315
|
3.7
|
18.4
|
1.0
|
OP2
|
D:0G6
|
4.0
|
17.4
|
1.0
|
O
|
A:HOH921
|
4.0
|
26.0
|
1.0
|
NZ
|
A:LYS701
|
4.0
|
19.7
|
1.0
|
CB
|
A:ASP705
|
4.0
|
15.4
|
1.0
|
OP1
|
D:0U5
|
4.1
|
17.7
|
1.0
|
OD1
|
A:ASP705
|
4.1
|
16.7
|
1.0
|
OP1
|
D:0G32
|
4.3
|
16.0
|
1.0
|
O5'
|
D:0U5
|
4.4
|
19.6
|
1.0
|
O
|
A:HOH910
|
4.5
|
23.5
|
1.0
|
C3'
|
D:0C31
|
4.5
|
13.0
|
1.0
|
O3'
|
D:0C31
|
4.6
|
15.4
|
1.0
|
O5'
|
D:0G32
|
4.6
|
16.9
|
1.0
|
MG
|
D:MG103
|
4.7
|
17.4
|
1.0
|
O3'
|
D:0U5
|
4.7
|
18.3
|
1.0
|
O5'
|
D:0G6
|
4.8
|
16.9
|
1.0
|
O
|
D:HOH255
|
4.8
|
18.0
|
1.0
|
C5'
|
D:0U5
|
4.8
|
18.6
|
1.0
|
O3'
|
D:0A4
|
4.8
|
17.5
|
1.0
|
NH2
|
A:ARG718
|
4.9
|
23.2
|
1.0
|
OP2
|
D:0C31
|
5.0
|
16.8
|
1.0
|
|
Calcium binding site 2 out
of 6 in 4wb2
Go back to
Calcium Binding Sites List in 4wb2
Calcium binding site 2 out
of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_02.jpg) Mono view
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca802
b:20.7
occ:0.99
|
OP1
|
E:0G32
|
2.3
|
23.6
|
1.0
|
O
|
E:HOH241
|
2.3
|
23.4
|
1.0
|
OP1
|
E:0U5
|
2.4
|
19.3
|
1.0
|
OD2
|
C:ASP705
|
2.5
|
27.3
|
1.0
|
O
|
E:HOH229
|
2.5
|
21.7
|
1.0
|
OP2
|
E:0G6
|
2.5
|
21.2
|
1.0
|
O
|
E:HOH226
|
2.5
|
21.3
|
1.0
|
CG
|
C:ASP705
|
3.4
|
25.1
|
1.0
|
P
|
E:0U5
|
3.7
|
20.4
|
1.0
|
P
|
E:0G6
|
3.7
|
22.6
|
1.0
|
P
|
E:0G32
|
3.7
|
24.1
|
1.0
|
O
|
E:HOH225
|
3.8
|
21.6
|
1.0
|
OP1
|
E:0G6
|
4.0
|
23.1
|
1.0
|
NZ
|
C:LYS701
|
4.0
|
23.5
|
1.0
|
CB
|
C:ASP705
|
4.1
|
25.7
|
1.0
|
O
|
C:HOH910
|
4.1
|
24.1
|
1.0
|
OP2
|
E:0U5
|
4.2
|
22.0
|
1.0
|
OD1
|
C:ASP705
|
4.2
|
25.3
|
1.0
|
OP2
|
E:0G32
|
4.3
|
21.1
|
1.0
|
O5'
|
E:0U5
|
4.4
|
21.4
|
1.0
|
O5'
|
E:0G32
|
4.6
|
24.5
|
1.0
|
O3'
|
E:0C31
|
4.7
|
22.2
|
1.0
|
C3'
|
E:0C31
|
4.7
|
22.4
|
1.0
|
MG
|
E:MG103
|
4.7
|
19.5
|
1.0
|
C5'
|
E:0U5
|
4.7
|
20.6
|
1.0
|
O5'
|
E:0G6
|
4.8
|
26.7
|
1.0
|
O
|
E:HOH234
|
4.8
|
22.3
|
1.0
|
O3'
|
E:0U5
|
4.8
|
20.5
|
1.0
|
O
|
C:HOH913
|
4.9
|
32.9
|
1.0
|
O3'
|
E:0A4
|
4.9
|
23.0
|
1.0
|
OP2
|
E:0C31
|
4.9
|
42.7
|
1.0
|
O2
|
E:3KA28
|
5.0
|
26.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 4wb2
Go back to
Calcium Binding Sites List in 4wb2
Calcium binding site 3 out
of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_03.jpg) Mono view
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca101
b:23.8
occ:1.00
|
O6
|
D:0G19
|
2.5
|
25.4
|
1.0
|
O6
|
D:0G27
|
2.5
|
19.6
|
1.0
|
O6
|
D:0G22
|
2.5
|
22.5
|
1.0
|
O6
|
D:0G18
|
2.5
|
22.2
|
1.0
|
O6
|
D:0G26
|
2.5
|
22.0
|
1.0
|
O6
|
D:0G32
|
2.5
|
18.2
|
1.0
|
O6
|
D:0G17
|
2.6
|
25.2
|
1.0
|
O6
|
D:0G25
|
2.6
|
25.7
|
1.0
|
C6
|
D:0G19
|
3.4
|
27.5
|
1.0
|
C6
|
D:0G22
|
3.5
|
23.4
|
1.0
|
C6
|
D:0G18
|
3.5
|
23.9
|
1.0
|
C6
|
D:0G27
|
3.5
|
20.8
|
1.0
|
C6
|
D:0G32
|
3.5
|
17.8
|
1.0
|
C6
|
D:0G26
|
3.5
|
19.1
|
1.0
|
C6
|
D:0G25
|
3.5
|
26.2
|
1.0
|
C6
|
D:0G17
|
3.5
|
23.6
|
1.0
|
N1
|
D:0G19
|
3.8
|
30.4
|
1.0
|
N1
|
D:0G26
|
3.8
|
20.2
|
1.0
|
N1
|
D:0G18
|
3.8
|
24.0
|
1.0
|
N1
|
D:0G22
|
3.8
|
26.0
|
1.0
|
N1
|
D:0G32
|
3.9
|
19.4
|
1.0
|
N1
|
D:0G27
|
3.9
|
21.2
|
1.0
|
N1
|
D:0G25
|
3.9
|
22.9
|
1.0
|
N1
|
D:0G17
|
4.0
|
24.9
|
1.0
|
N1
|
D:0A16
|
4.5
|
29.1
|
1.0
|
C6
|
D:0A16
|
4.6
|
28.4
|
1.0
|
C5
|
D:0G19
|
4.7
|
30.2
|
1.0
|
C5
|
D:0G22
|
4.7
|
29.0
|
1.0
|
C5
|
D:0G18
|
4.7
|
25.0
|
1.0
|
C5
|
D:0G25
|
4.7
|
26.0
|
1.0
|
C5
|
D:0G32
|
4.7
|
20.0
|
1.0
|
C5
|
D:0G27
|
4.7
|
18.5
|
1.0
|
C5
|
D:0G17
|
4.7
|
23.1
|
1.0
|
C5
|
D:0G26
|
4.7
|
19.2
|
1.0
|
C2
|
D:0A16
|
4.8
|
28.8
|
1.0
|
N6
|
D:0A16
|
5.0
|
29.0
|
1.0
|
CB
|
A:SER697
|
5.0
|
24.9
|
1.0
|
|
Calcium binding site 4 out
of 6 in 4wb2
Go back to
Calcium Binding Sites List in 4wb2
Calcium binding site 4 out
of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_04.jpg) Mono view
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca102
b:25.1
occ:0.85
|
OP2
|
D:0C34
|
2.3
|
20.6
|
1.0
|
O
|
D:HOH270
|
2.4
|
28.3
|
1.0
|
O
|
D:HOH297
|
2.4
|
25.9
|
1.0
|
O
|
D:HOH261
|
2.5
|
20.7
|
1.0
|
O
|
D:HOH267
|
2.5
|
24.9
|
1.0
|
O
|
D:HOH272
|
2.6
|
22.2
|
1.0
|
O
|
D:HOH262
|
2.6
|
21.0
|
1.0
|
P
|
D:0C34
|
3.7
|
21.8
|
1.0
|
OP1
|
D:0A33
|
4.2
|
17.5
|
1.0
|
O
|
D:HOH266
|
4.2
|
20.2
|
1.0
|
O5'
|
D:0C34
|
4.3
|
23.3
|
1.0
|
O6
|
D:0G6
|
4.3
|
18.1
|
1.0
|
C5
|
D:0C34
|
4.4
|
21.5
|
1.0
|
OP1
|
D:0C34
|
4.4
|
26.6
|
1.0
|
N4
|
D:0C36
|
4.4
|
19.3
|
1.0
|
O
|
D:HOH250
|
4.4
|
15.6
|
1.0
|
O
|
D:HOH302
|
4.5
|
35.1
|
1.0
|
OP2
|
D:0A33
|
4.7
|
18.1
|
1.0
|
O
|
D:HOH268
|
4.7
|
28.3
|
1.0
|
N7
|
D:0G35
|
4.7
|
20.2
|
1.0
|
C6
|
D:0C34
|
4.8
|
20.8
|
1.0
|
O
|
D:HOH327
|
4.8
|
47.8
|
1.0
|
O3'
|
D:0A33
|
4.8
|
23.3
|
1.0
|
O
|
D:HOH259
|
4.9
|
16.9
|
1.0
|
O
|
D:HOH287
|
4.9
|
35.5
|
1.0
|
P
|
D:0A33
|
5.0
|
19.3
|
1.0
|
OP2
|
D:0A4
|
5.0
|
22.8
|
1.0
|
|
Calcium binding site 5 out
of 6 in 4wb2
Go back to
Calcium Binding Sites List in 4wb2
Calcium binding site 5 out
of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_05.jpg) Mono view
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca101
b:24.7
occ:0.97
|
O6
|
E:0G19
|
2.4
|
31.2
|
1.0
|
O6
|
E:0G27
|
2.5
|
34.0
|
1.0
|
O6
|
E:0G18
|
2.5
|
28.1
|
1.0
|
O6
|
E:0G26
|
2.5
|
30.8
|
1.0
|
O6
|
E:0G32
|
2.5
|
28.7
|
1.0
|
O6
|
E:0G17
|
2.5
|
29.4
|
1.0
|
O6
|
E:0G22
|
2.5
|
30.9
|
1.0
|
O6
|
E:0G25
|
2.6
|
32.1
|
1.0
|
C6
|
E:0G19
|
3.4
|
34.1
|
1.0
|
C6
|
E:0G27
|
3.4
|
30.3
|
1.0
|
C6
|
E:0G32
|
3.4
|
26.8
|
1.0
|
C6
|
E:0G18
|
3.5
|
30.6
|
1.0
|
C6
|
E:0G22
|
3.5
|
31.2
|
1.0
|
C6
|
E:0G17
|
3.5
|
30.2
|
1.0
|
C6
|
E:0G26
|
3.5
|
27.8
|
1.0
|
C6
|
E:0G25
|
3.6
|
38.5
|
1.0
|
N1
|
E:0G27
|
3.8
|
27.3
|
1.0
|
N1
|
E:0G32
|
3.8
|
25.6
|
1.0
|
N1
|
E:0G19
|
3.8
|
34.9
|
1.0
|
N1
|
E:0G22
|
3.9
|
32.5
|
1.0
|
N1
|
E:0G26
|
3.9
|
26.9
|
1.0
|
N1
|
E:0G18
|
3.9
|
29.6
|
1.0
|
N1
|
E:0G17
|
3.9
|
29.8
|
1.0
|
N1
|
E:0G25
|
4.0
|
36.1
|
1.0
|
N1
|
E:0A16
|
4.4
|
41.1
|
1.0
|
C2
|
E:0A16
|
4.6
|
40.6
|
1.0
|
C5
|
E:0G27
|
4.6
|
30.0
|
1.0
|
C5
|
E:0G19
|
4.7
|
33.8
|
1.0
|
C5
|
E:0G32
|
4.7
|
27.4
|
1.0
|
C6
|
E:0A16
|
4.7
|
40.6
|
1.0
|
C5
|
E:0G17
|
4.7
|
30.2
|
1.0
|
C5
|
E:0G18
|
4.7
|
28.4
|
1.0
|
C5
|
E:0G22
|
4.7
|
33.0
|
1.0
|
C5
|
E:0G26
|
4.8
|
29.5
|
1.0
|
C5
|
E:0G25
|
4.8
|
35.1
|
1.0
|
|
Calcium binding site 6 out
of 6 in 4wb2
Go back to
Calcium Binding Sites List in 4wb2
Calcium binding site 6 out
of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_06.jpg) Mono view
![](/pictures/CA/pdb/wb/4wb2-CA-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca102
b:27.8
occ:0.91
|
O
|
E:HOH265
|
2.4
|
27.8
|
1.0
|
OP1
|
E:0C34
|
2.4
|
27.7
|
1.0
|
O
|
E:HOH261
|
2.4
|
27.4
|
1.0
|
O
|
E:HOH243
|
2.4
|
25.4
|
1.0
|
O
|
E:HOH258
|
2.5
|
33.6
|
1.0
|
O
|
E:HOH246
|
2.6
|
26.4
|
1.0
|
O
|
E:HOH236
|
2.6
|
28.9
|
1.0
|
P
|
E:0C34
|
3.8
|
31.0
|
1.0
|
OP2
|
E:0A33
|
4.0
|
27.0
|
1.0
|
O
|
E:HOH253
|
4.1
|
29.7
|
1.0
|
C5
|
E:0C34
|
4.3
|
26.4
|
1.0
|
O
|
E:HOH224
|
4.3
|
20.0
|
1.0
|
O5'
|
E:0C34
|
4.4
|
34.0
|
1.0
|
O6
|
E:0G6
|
4.4
|
23.8
|
1.0
|
O
|
E:HOH248
|
4.4
|
36.2
|
1.0
|
N4
|
E:0C36
|
4.5
|
29.2
|
1.0
|
O
|
E:HOH297
|
4.5
|
39.3
|
1.0
|
OP2
|
E:0C34
|
4.6
|
33.5
|
1.0
|
N7
|
E:0G35
|
4.7
|
25.2
|
1.0
|
OP1
|
E:0A33
|
4.7
|
27.6
|
1.0
|
C6
|
E:0C34
|
4.7
|
27.5
|
1.0
|
P
|
E:0A33
|
4.9
|
27.6
|
1.0
|
O
|
E:HOH230
|
4.9
|
21.2
|
1.0
|
OP1
|
E:0A4
|
4.9
|
26.4
|
1.0
|
O3'
|
E:0A33
|
5.0
|
28.4
|
1.0
|
O6
|
E:0G35
|
5.0
|
26.3
|
1.0
|
O
|
E:HOH270
|
5.0
|
39.1
|
1.0
|
|
Reference:
L.Yatime,
C.Maasch,
K.Hoehlig,
S.Klussmann,
G.R.Andersen,
A.Vater.
Structural Basis For the Targeting of Complement Anaphylatoxin C5A Using A Mixed L-Rna/L-Dna Aptamer. Nat Commun V. 6 6481 2015.
ISSN: ESSN 2041-1723
PubMed: 25901944
DOI: 10.1038/NCOMMS7481
Page generated: Sun Jul 14 14:03:33 2024
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