Calcium in PDB 244d: The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Protein crystallography data
The structure of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex, PDB code: 244d
was solved by
G.Laughlan,
A.I.H.Murchie,
D.G.Norman,
M.H.Moore,
P.C.E.Moody,
D.M.J.Lilley,
B.Luisi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.20
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
28.760,
35.470,
56.770,
74.39,
77.64,
89.73
|
R / Rfree (%)
|
12.4 /
17.6
|
Other elements in 244d:
The structure of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
(pdb code 244d). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the
The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex, PDB code: 244d:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Calcium binding site 1 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 1 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca177
b:8.4
occ:1.00
|
O
|
D:HOH420
|
2.4
|
23.2
|
1.0
|
O
|
A:HOH182
|
2.4
|
8.1
|
1.0
|
O
|
D:HOH321
|
2.4
|
21.1
|
1.0
|
O
|
D:HOH196
|
2.4
|
8.7
|
1.0
|
O
|
D:HOH300
|
2.4
|
19.1
|
1.0
|
O
|
D:HOH339
|
2.4
|
22.0
|
1.0
|
O
|
D:HOH186
|
2.5
|
8.6
|
1.0
|
O
|
G:HOH185
|
2.5
|
9.3
|
1.0
|
OP2
|
D:DG32
|
4.3
|
9.6
|
1.0
|
OP1
|
D:DG32
|
4.4
|
8.9
|
1.0
|
O
|
F:HOH235
|
4.4
|
11.0
|
1.0
|
N2
|
A:DG2
|
4.5
|
5.8
|
1.0
|
N2
|
G:DG62
|
4.5
|
7.3
|
1.0
|
O
|
F:HOH600
|
4.5
|
37.3
|
1.0
|
O4'
|
A:DG3
|
4.5
|
7.7
|
1.0
|
O
|
F:HOH357
|
4.6
|
28.7
|
1.0
|
O4'
|
G:DG63
|
4.6
|
10.2
|
1.0
|
O
|
D:HOH595
|
4.7
|
35.7
|
1.0
|
O
|
D:HOH303
|
4.8
|
26.2
|
1.0
|
O
|
D:HOH341
|
4.8
|
27.9
|
1.0
|
P
|
D:DG32
|
4.9
|
7.8
|
1.0
|
N3
|
A:DG2
|
4.9
|
5.4
|
1.0
|
N3
|
G:DG62
|
4.9
|
7.0
|
1.0
|
C4'
|
A:DG3
|
4.9
|
7.8
|
1.0
|
O
|
G:HOH302
|
4.9
|
23.2
|
1.0
|
|
Calcium binding site 2 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 2 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca179
b:11.1
occ:1.00
|
O
|
D:HOH292
|
2.4
|
17.1
|
1.0
|
O
|
D:HOH233
|
2.4
|
16.1
|
1.0
|
O
|
D:HOH227
|
2.4
|
13.1
|
1.0
|
O
|
D:HOH276
|
2.5
|
16.7
|
1.0
|
O
|
A:HOH323
|
2.5
|
16.6
|
1.0
|
O
|
D:HOH298
|
2.5
|
16.9
|
1.0
|
O
|
D:HOH231
|
2.5
|
12.5
|
1.0
|
OP2
|
D:DG34
|
4.4
|
13.6
|
1.0
|
O3'
|
A:DG5
|
4.5
|
10.8
|
1.0
|
OP1
|
D:DG33
|
4.5
|
11.0
|
1.0
|
C4'
|
A:DG5
|
4.5
|
10.0
|
1.0
|
O
|
D:HOH248
|
4.7
|
13.9
|
1.0
|
OP1
|
A:DT6
|
4.8
|
14.5
|
1.0
|
OP2
|
D:DG33
|
4.8
|
10.4
|
1.0
|
O
|
D:HOH512
|
4.9
|
38.4
|
1.0
|
|
Calcium binding site 3 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 3 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca178
b:7.1
occ:1.00
|
O
|
A:HOH180
|
2.4
|
8.3
|
1.0
|
O
|
B:HOH193
|
2.4
|
7.6
|
1.0
|
O
|
A:HOH266
|
2.4
|
14.7
|
1.0
|
O
|
E:HOH220
|
2.4
|
10.3
|
1.0
|
O
|
I:HOH218
|
2.4
|
12.2
|
1.0
|
O
|
F:HOH183
|
2.5
|
7.5
|
1.0
|
O
|
A:HOH181
|
2.5
|
7.5
|
1.0
|
O
|
B:HOH210
|
4.3
|
12.4
|
1.0
|
OP2
|
A:DG2
|
4.3
|
10.5
|
1.0
|
N2
|
F:DG52
|
4.4
|
6.4
|
1.0
|
N2
|
B:DG12
|
4.5
|
6.8
|
1.0
|
O
|
A:HOH279
|
4.5
|
22.6
|
1.0
|
O
|
I:HOH224
|
4.5
|
12.8
|
1.0
|
OP1
|
A:DG2
|
4.5
|
9.9
|
1.0
|
O
|
A:HOH254
|
4.6
|
17.7
|
1.0
|
O4'
|
B:DG13
|
4.6
|
8.4
|
1.0
|
O
|
E:HOH230
|
4.6
|
12.0
|
1.0
|
O4'
|
F:DG53
|
4.6
|
8.0
|
1.0
|
C4'
|
B:DG13
|
4.8
|
9.4
|
1.0
|
N3
|
F:DG52
|
4.9
|
5.9
|
1.0
|
O5'
|
E:DT41
|
4.9
|
11.6
|
1.0
|
O
|
E:HOH386
|
4.9
|
23.0
|
1.0
|
N3
|
B:DG12
|
4.9
|
5.6
|
1.0
|
C5'
|
B:DG13
|
4.9
|
10.3
|
1.0
|
P
|
A:DG2
|
5.0
|
9.2
|
1.0
|
O
|
I:HOH282
|
5.0
|
17.5
|
1.0
|
|
Calcium binding site 4 out
of 9 in 244d
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Calcium Binding Sites List in 244d
Calcium binding site 4 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca176
b:9.2
occ:1.00
|
O
|
C:HOH191
|
2.4
|
10.2
|
1.0
|
O
|
B:HOH428
|
2.4
|
21.5
|
1.0
|
O
|
B:HOH215
|
2.4
|
9.4
|
1.0
|
O
|
B:HOH356
|
2.4
|
27.8
|
1.0
|
O
|
B:HOH400
|
2.4
|
22.0
|
1.0
|
O
|
E:HOH197
|
2.5
|
9.7
|
1.0
|
O
|
B:HOH187
|
2.5
|
8.9
|
1.0
|
O
|
E:HOH382
|
2.6
|
29.0
|
1.0
|
N2
|
E:DG42
|
4.4
|
8.2
|
1.0
|
OP2
|
B:DG12
|
4.4
|
9.9
|
1.0
|
N2
|
C:DG22
|
4.5
|
5.7
|
1.0
|
O
|
C:HOH273
|
4.5
|
14.8
|
1.0
|
OP1
|
B:DG12
|
4.5
|
9.7
|
1.0
|
O4'
|
C:DG23
|
4.5
|
9.6
|
1.0
|
O4'
|
E:DG43
|
4.5
|
9.9
|
1.0
|
O
|
B:HOH435
|
4.6
|
42.6
|
1.0
|
O
|
B:HOH283
|
4.6
|
21.6
|
1.0
|
O
|
B:HOH344
|
4.7
|
19.3
|
1.0
|
C4'
|
C:DG23
|
4.8
|
10.6
|
1.0
|
N3
|
E:DG42
|
4.9
|
6.5
|
1.0
|
O
|
E:HOH295
|
4.9
|
24.9
|
1.0
|
N3
|
C:DG22
|
4.9
|
5.5
|
1.0
|
P
|
B:DG12
|
4.9
|
9.1
|
1.0
|
|
Calcium binding site 5 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 5 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca175
b:9.5
occ:1.00
|
O
|
D:HOH256
|
2.4
|
11.5
|
1.0
|
O
|
C:HOH507
|
2.4
|
19.2
|
1.0
|
O
|
C:HOH190
|
2.4
|
10.7
|
1.0
|
O
|
C:HOH234
|
2.4
|
17.7
|
1.0
|
O
|
H:HOH232
|
2.5
|
10.7
|
1.0
|
O
|
D:HOH222
|
2.5
|
10.4
|
1.0
|
OP2
|
C:DG22
|
4.3
|
12.2
|
1.0
|
O
|
D:HOH239
|
4.4
|
13.4
|
1.0
|
N2
|
D:DG32
|
4.4
|
7.6
|
1.0
|
N2
|
H:DG72
|
4.4
|
8.1
|
1.0
|
O4'
|
D:DG33
|
4.5
|
9.8
|
1.0
|
OP1
|
C:DG22
|
4.6
|
13.9
|
1.0
|
O
|
C:HOH473
|
4.6
|
31.5
|
1.0
|
O4'
|
H:DG73
|
4.8
|
13.0
|
1.0
|
N3
|
D:DG32
|
4.8
|
5.6
|
1.0
|
N3
|
H:DG72
|
4.9
|
7.6
|
1.0
|
O
|
H:HOH330
|
4.9
|
33.2
|
1.0
|
P
|
C:DG22
|
4.9
|
11.3
|
1.0
|
C4'
|
D:DG33
|
5.0
|
9.9
|
1.0
|
|
Calcium binding site 6 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 6 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ca174
b:7.8
occ:1.00
|
O
|
L:HOH261
|
2.4
|
12.4
|
1.0
|
O
|
O:HOH229
|
2.4
|
10.1
|
1.0
|
O
|
N:HOH201
|
2.4
|
8.2
|
1.0
|
O
|
L:HOH244
|
2.4
|
13.3
|
1.0
|
O
|
N:HOH207
|
2.5
|
7.7
|
1.0
|
O
|
L:HOH228
|
2.5
|
9.5
|
1.0
|
OP2
|
N:DG132
|
4.3
|
10.2
|
1.0
|
N2
|
L:DG112
|
4.4
|
7.2
|
1.0
|
O
|
O:HOH255
|
4.4
|
14.7
|
1.0
|
N2
|
O:DG142
|
4.4
|
7.1
|
1.0
|
O
|
L:HOH290
|
4.4
|
21.0
|
1.0
|
OP1
|
N:DG132
|
4.5
|
12.0
|
1.0
|
O4'
|
O:DG143
|
4.7
|
8.2
|
1.0
|
O4'
|
L:DG113
|
4.8
|
11.1
|
1.0
|
O
|
L:HOH296
|
4.8
|
25.4
|
1.0
|
N3
|
O:DG142
|
4.8
|
6.3
|
1.0
|
O
|
L:HOH360
|
4.8
|
29.7
|
1.0
|
N3
|
L:DG112
|
4.9
|
6.0
|
1.0
|
P
|
N:DG132
|
4.9
|
9.4
|
1.0
|
|
Calcium binding site 7 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 7 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Ca171
b:7.9
occ:1.00
|
O
|
P:HOH253
|
2.3
|
24.0
|
1.0
|
O
|
P:HOH541
|
2.4
|
18.7
|
1.0
|
O
|
M:HOH188
|
2.4
|
8.6
|
1.0
|
O
|
P:HOH267
|
2.4
|
16.3
|
1.0
|
O
|
P:HOH213
|
2.4
|
8.5
|
1.0
|
O
|
J:HOH206
|
2.4
|
9.5
|
1.0
|
O
|
P:HOH198
|
2.5
|
7.6
|
1.0
|
N2
|
J:DG92
|
4.4
|
7.4
|
1.0
|
O
|
P:HOH534
|
4.4
|
23.8
|
1.0
|
O
|
M:HOH211
|
4.4
|
9.9
|
1.0
|
O
|
P:HOH240
|
4.4
|
16.9
|
1.0
|
O
|
E:HOH613
|
4.5
|
38.5
|
1.0
|
N2
|
M:DG122
|
4.5
|
6.5
|
1.0
|
OP2
|
P:DG152
|
4.5
|
10.0
|
1.0
|
O4'
|
M:DG123
|
4.5
|
8.3
|
1.0
|
OP1
|
P:DG152
|
4.5
|
11.6
|
1.0
|
O4'
|
J:DG93
|
4.6
|
9.5
|
1.0
|
O
|
E:HOH464
|
4.7
|
31.9
|
1.0
|
C4'
|
M:DG123
|
4.8
|
9.3
|
1.0
|
O
|
J:HOH331
|
4.8
|
21.3
|
1.0
|
N3
|
M:DG122
|
4.8
|
5.8
|
1.0
|
N3
|
J:DG92
|
4.9
|
7.0
|
1.0
|
O
|
I:HOH280
|
4.9
|
19.4
|
1.0
|
C5'
|
M:DG123
|
5.0
|
9.7
|
1.0
|
P
|
P:DG152
|
5.0
|
8.7
|
1.0
|
|
Calcium binding site 8 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 8 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Ca173
b:7.7
occ:1.00
|
O
|
M:HOH293
|
2.4
|
17.1
|
1.0
|
O
|
N:HOH184
|
2.4
|
8.1
|
1.0
|
O
|
M:HOH291
|
2.4
|
19.9
|
1.0
|
O
|
M:HOH216
|
2.4
|
8.9
|
1.0
|
O
|
M:HOH195
|
2.5
|
7.4
|
1.0
|
O
|
I:HOH189
|
2.5
|
7.9
|
1.0
|
O
|
M:HOH373
|
2.5
|
20.2
|
1.0
|
O
|
M:HOH402
|
2.5
|
24.2
|
1.0
|
O
|
M:HOH616
|
4.3
|
41.4
|
1.0
|
OP1
|
M:DG122
|
4.4
|
8.5
|
1.0
|
OP2
|
M:DG122
|
4.4
|
8.5
|
1.0
|
O
|
L:HOH260
|
4.4
|
12.6
|
1.0
|
N2
|
I:DG82
|
4.4
|
6.4
|
1.0
|
N2
|
N:DG132
|
4.5
|
6.2
|
1.0
|
O4'
|
N:DG133
|
4.5
|
7.8
|
1.0
|
O
|
M:HOH558
|
4.6
|
31.8
|
1.0
|
O4'
|
I:DG83
|
4.7
|
9.1
|
1.0
|
O
|
L:HOH432
|
4.7
|
30.7
|
1.0
|
O
|
M:HOH421
|
4.7
|
32.4
|
1.0
|
O
|
M:HOH691
|
4.7
|
25.7
|
1.0
|
O
|
I:HOH309
|
4.9
|
20.0
|
1.0
|
N3
|
N:DG132
|
4.9
|
5.3
|
1.0
|
P
|
M:DG122
|
4.9
|
7.3
|
1.0
|
N3
|
I:DG82
|
4.9
|
5.8
|
1.0
|
C4'
|
N:DG133
|
4.9
|
7.3
|
1.0
|
|
Calcium binding site 9 out
of 9 in 244d
Go back to
Calcium Binding Sites List in 244d
Calcium binding site 9 out
of 9 in the The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of The High-Resolution Crystal Structure of A Parallel- Stranded Guanine Tetraplex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Ca172
b:9.4
occ:1.00
|
O
|
P:HOH192
|
2.4
|
10.1
|
1.0
|
O
|
O:HOH202
|
2.4
|
10.3
|
1.0
|
O
|
O:HOH199
|
2.4
|
9.1
|
1.0
|
O
|
O:HOH392
|
2.5
|
21.3
|
1.0
|
O
|
K:HOH226
|
2.5
|
9.8
|
1.0
|
O
|
P:HOH364
|
2.5
|
19.4
|
1.0
|
O
|
O:HOH460
|
2.5
|
24.9
|
1.0
|
O
|
O:HOH409
|
2.5
|
27.8
|
1.0
|
OP2
|
O:DG142
|
4.4
|
11.4
|
1.0
|
N2
|
K:DG102
|
4.4
|
7.8
|
1.0
|
OP1
|
O:DG142
|
4.4
|
10.8
|
1.0
|
O
|
P:HOH275
|
4.4
|
14.7
|
1.0
|
O4'
|
P:DG153
|
4.5
|
9.4
|
1.0
|
N2
|
P:DG152
|
4.5
|
6.6
|
1.0
|
O4'
|
K:DG103
|
4.6
|
11.7
|
1.0
|
O
|
O:HOH308
|
4.7
|
21.8
|
1.0
|
C4'
|
P:DG153
|
4.8
|
10.1
|
1.0
|
O
|
K:HOH325
|
4.8
|
25.3
|
1.0
|
O
|
O:HOH395
|
4.8
|
27.1
|
1.0
|
O
|
O:HOH372
|
4.9
|
21.3
|
1.0
|
N3
|
K:DG102
|
4.9
|
7.0
|
1.0
|
N3
|
P:DG152
|
4.9
|
5.9
|
1.0
|
P
|
O:DG142
|
5.0
|
10.2
|
1.0
|
|
Reference:
G.Laughlan,
A.I.Murchie,
D.G.Norman,
M.H.Moore,
P.C.Moody,
D.M.Lilley,
B.Luisi.
The High-Resolution Crystal Structure of A Parallel-Stranded Guanine Tetraplex. Science V. 265 520 1994.
ISSN: ISSN 0036-8075
PubMed: 8036494
Page generated: Fri Jul 12 08:30:10 2024
|