Magnesium in PDB 7eog: Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak
Protein crystallography data
The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak, PDB code: 7eog
was solved by
K.Y.Huang,
A.M.Ren,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.07 /
1.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.925,
34.771,
58.552,
90,
128.11,
90
|
R / Rfree (%)
|
19.2 /
21.8
|
Other elements in 7eog:
The structure of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak
(pdb code 7eog). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak, PDB code: 7eog:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7eog
Go back to
Magnesium Binding Sites List in 7eog
Magnesium binding site 1 out
of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg103
b:16.7
occ:1.00
|
O
|
A:HOH287
|
2.1
|
16.3
|
1.0
|
OP2
|
A:A30
|
2.1
|
17.1
|
1.0
|
O
|
A:HOH236
|
2.2
|
16.9
|
1.0
|
O
|
A:HOH248
|
2.2
|
15.4
|
1.0
|
O
|
A:HOH286
|
2.2
|
15.7
|
1.0
|
O
|
A:HOH346
|
2.2
|
14.1
|
1.0
|
P
|
A:A30
|
3.5
|
17.2
|
1.0
|
O
|
A:HOH367
|
3.8
|
14.6
|
1.0
|
O5'
|
A:A30
|
3.8
|
16.5
|
1.0
|
O
|
A:HOH303
|
4.0
|
17.9
|
1.0
|
O
|
A:HOH223
|
4.1
|
16.1
|
1.0
|
O4
|
A:U32
|
4.1
|
16.8
|
1.0
|
N7
|
A:A30
|
4.2
|
18.0
|
1.0
|
O
|
A:HOH227
|
4.2
|
20.7
|
1.0
|
C8
|
A:A30
|
4.3
|
16.4
|
1.0
|
N7
|
A:A31
|
4.3
|
16.5
|
1.0
|
O
|
A:HOH239
|
4.3
|
15.5
|
1.0
|
OP1
|
A:G37
|
4.4
|
19.2
|
1.0
|
OP1
|
A:A30
|
4.4
|
14.8
|
1.0
|
OP1
|
A:C29
|
4.4
|
18.4
|
1.0
|
O3'
|
A:C29
|
4.5
|
16.1
|
1.0
|
N6
|
A:A31
|
4.6
|
19.3
|
1.0
|
OP2
|
A:A31
|
4.7
|
15.4
|
1.0
|
C3'
|
A:C29
|
4.7
|
17.2
|
1.0
|
O5'
|
A:C29
|
4.9
|
19.0
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7eog
Go back to
Magnesium Binding Sites List in 7eog
Magnesium binding site 2 out
of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg104
b:17.8
occ:1.00
|
OP2
|
A:U32
|
2.1
|
16.8
|
1.0
|
O
|
A:HOH268
|
2.1
|
16.0
|
1.0
|
O
|
A:HOH278
|
2.1
|
16.0
|
1.0
|
O
|
A:HOH330
|
2.1
|
14.4
|
1.0
|
O
|
A:HOH364
|
2.2
|
17.9
|
1.0
|
O
|
A:HOH235
|
2.2
|
15.7
|
1.0
|
P
|
A:U32
|
3.4
|
16.6
|
1.0
|
O
|
A:HOH348
|
3.6
|
32.6
|
1.0
|
O5'
|
A:U32
|
3.9
|
18.1
|
1.0
|
O
|
A:HOH340
|
4.1
|
16.0
|
1.0
|
OP1
|
A:A31
|
4.1
|
15.8
|
1.0
|
OP1
|
A:U32
|
4.2
|
18.7
|
1.0
|
OP2
|
A:G34
|
4.3
|
16.6
|
1.0
|
OP2
|
A:C33
|
4.4
|
18.4
|
1.0
|
OP1
|
A:G34
|
4.4
|
17.4
|
1.0
|
O
|
A:HOH241
|
4.4
|
26.0
|
1.0
|
C5
|
A:U32
|
4.5
|
15.6
|
1.0
|
OP2
|
A:A31
|
4.5
|
15.4
|
1.0
|
O3'
|
A:A31
|
4.6
|
17.4
|
1.0
|
P
|
A:A31
|
4.6
|
15.2
|
1.0
|
C6
|
A:U32
|
4.7
|
14.7
|
1.0
|
O5'
|
A:A31
|
4.7
|
16.5
|
1.0
|
P
|
A:G34
|
4.8
|
15.6
|
1.0
|
C3'
|
A:A31
|
4.9
|
15.1
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7eog
Go back to
Magnesium Binding Sites List in 7eog
Magnesium binding site 3 out
of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg105
b:20.1
occ:1.00
|
OP2
|
A:U42
|
2.1
|
21.7
|
1.0
|
O
|
A:HOH359
|
2.1
|
20.3
|
1.0
|
O
|
A:HOH250
|
2.1
|
19.0
|
1.0
|
O
|
A:HOH279
|
2.1
|
16.2
|
1.0
|
O
|
A:HOH361
|
2.2
|
21.4
|
1.0
|
O
|
A:HOH333
|
2.2
|
20.5
|
1.0
|
P
|
A:U42
|
3.4
|
20.4
|
1.0
|
O5'
|
A:U42
|
3.9
|
20.9
|
1.0
|
O
|
A:HOH283
|
4.0
|
19.4
|
1.0
|
O3'
|
A:G41
|
4.1
|
18.6
|
1.0
|
O
|
A:HOH253
|
4.2
|
21.2
|
1.0
|
O2'
|
A:G41
|
4.2
|
17.8
|
1.0
|
O
|
A:HOH261
|
4.2
|
20.5
|
1.0
|
O
|
A:HOH285
|
4.4
|
21.8
|
1.0
|
O6
|
A:G4
|
4.4
|
16.5
|
1.0
|
N4
|
A:C3
|
4.5
|
15.5
|
1.0
|
O
|
A:HOH377
|
4.5
|
27.0
|
1.0
|
N4
|
A:C5
|
4.6
|
15.7
|
1.0
|
O
|
A:HOH351
|
4.6
|
33.1
|
1.0
|
OP1
|
A:U42
|
4.6
|
25.0
|
1.0
|
N7
|
A:G4
|
4.6
|
17.4
|
1.0
|
O
|
A:HOH325
|
4.7
|
16.6
|
1.0
|
C5
|
A:C3
|
4.7
|
14.1
|
1.0
|
C3'
|
A:G41
|
4.8
|
19.9
|
1.0
|
C4
|
A:C3
|
5.0
|
12.7
|
1.0
|
C2'
|
A:G41
|
5.0
|
18.7
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7eog
Go back to
Magnesium Binding Sites List in 7eog
Magnesium binding site 4 out
of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg106
b:16.3
occ:1.00
|
OP2
|
A:U8
|
2.0
|
16.0
|
1.0
|
OP2
|
A:C7
|
2.1
|
15.8
|
1.0
|
N7
|
A:G9
|
2.1
|
15.1
|
1.0
|
O
|
A:HOH327
|
2.1
|
16.7
|
1.0
|
O
|
A:HOH324
|
2.1
|
15.9
|
1.0
|
O
|
A:HOH350
|
2.2
|
18.3
|
1.0
|
C8
|
A:G9
|
3.0
|
14.7
|
1.0
|
C5
|
A:G9
|
3.2
|
15.4
|
1.0
|
P
|
A:U8
|
3.4
|
17.0
|
1.0
|
P
|
A:C7
|
3.5
|
16.2
|
1.0
|
O6
|
A:G9
|
3.7
|
15.8
|
1.0
|
O
|
A:HOH374
|
3.8
|
22.2
|
1.0
|
C6
|
A:G9
|
3.8
|
15.3
|
1.0
|
OP1
|
A:C7
|
4.1
|
16.1
|
1.0
|
O3'
|
A:C7
|
4.1
|
16.5
|
1.0
|
C5
|
A:U8
|
4.1
|
15.8
|
1.0
|
O
|
A:HOH249
|
4.1
|
26.2
|
1.0
|
O
|
A:HOH297
|
4.2
|
16.8
|
1.0
|
N9
|
A:G9
|
4.2
|
14.3
|
1.0
|
OP1
|
A:U8
|
4.3
|
16.2
|
1.0
|
O5'
|
A:U8
|
4.3
|
16.4
|
1.0
|
O5'
|
A:C7
|
4.3
|
16.6
|
1.0
|
C4
|
A:G9
|
4.4
|
15.6
|
1.0
|
O3'
|
A:A6
|
4.4
|
16.6
|
1.0
|
C3'
|
A:C7
|
4.5
|
14.9
|
1.0
|
C5'
|
A:C7
|
4.6
|
17.5
|
1.0
|
C6
|
A:U8
|
4.6
|
14.9
|
1.0
|
O
|
A:HOH260
|
4.7
|
25.6
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7eog
Go back to
Magnesium Binding Sites List in 7eog
Magnesium binding site 5 out
of 5 in the Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the Pepper Aptamer in Complex with Hbc, Iridium Hexammine Soak within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg107
b:28.0
occ:1.00
|
O
|
A:HOH311
|
1.9
|
21.6
|
1.0
|
O
|
A:HOH391
|
2.1
|
29.1
|
1.0
|
O
|
A:HOH231
|
2.3
|
22.7
|
1.0
|
O
|
A:HOH218
|
3.8
|
23.3
|
1.0
|
N4
|
A:C48
|
4.0
|
18.5
|
1.0
|
O
|
A:HOH358
|
4.1
|
26.0
|
1.0
|
O
|
A:HOH292
|
4.2
|
22.6
|
1.0
|
N7
|
A:G47
|
4.3
|
16.1
|
1.0
|
O
|
A:HOH363
|
4.3
|
26.0
|
1.0
|
O6
|
A:G47
|
4.4
|
17.1
|
1.0
|
O
|
A:HOH244
|
4.4
|
25.4
|
1.0
|
O
|
A:HOH319
|
4.7
|
32.2
|
1.0
|
C5
|
A:C46
|
4.9
|
19.3
|
1.0
|
C5
|
A:G47
|
4.9
|
16.2
|
1.0
|
N4
|
A:C46
|
4.9
|
17.8
|
1.0
|
C6
|
A:G47
|
5.0
|
16.1
|
1.0
|
|
Reference:
K.Huang,
X.Chen,
C.Li,
Q.Song,
H.Li,
L.Zhu,
Y.Yang,
A.Ren.
Structure-Based Investigation of Fluorogenic Pepper Aptamer. Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
PubMed: 34725509
DOI: 10.1038/S41589-021-00884-6
Page generated: Wed Oct 2 20:51:36 2024
|