Magnesium in PDB 5kpy: Structure of A 5-Hydroxytryptophan Aptamer
Protein crystallography data
The structure of Structure of A 5-Hydroxytryptophan Aptamer, PDB code: 5kpy
was solved by
R.T.Batey,
E.Porter,
M.Merck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
18.33 /
2.00
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.553,
26.594,
63.367,
90.00,
106.32,
90.00
|
R / Rfree (%)
|
21.7 /
25.8
|
Other elements in 5kpy:
The structure of Structure of A 5-Hydroxytryptophan Aptamer also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of A 5-Hydroxytryptophan Aptamer
(pdb code 5kpy). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Structure of A 5-Hydroxytryptophan Aptamer, PDB code: 5kpy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 5kpy
Go back to
Magnesium Binding Sites List in 5kpy
Magnesium binding site 1 out
of 6 in the Structure of A 5-Hydroxytryptophan Aptamer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg114
b:17.3
occ:1.00
|
O2
|
A:C77
|
4.3
|
25.3
|
1.0
|
O2'
|
A:C77
|
4.5
|
29.7
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 5kpy
Go back to
Magnesium Binding Sites List in 5kpy
Magnesium binding site 2 out
of 6 in the Structure of A 5-Hydroxytryptophan Aptamer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg115
b:40.2
occ:1.00
|
O
|
A:HOH251
|
3.0
|
36.2
|
0.8
|
O
|
A:HOH308
|
3.4
|
33.9
|
1.0
|
OP2
|
A:C77
|
3.6
|
28.7
|
1.0
|
O
|
A:HOH268
|
4.1
|
27.8
|
0.8
|
N7
|
A:G78
|
4.2
|
28.3
|
1.0
|
P
|
A:C77
|
4.5
|
30.6
|
1.0
|
OP1
|
A:C77
|
4.5
|
32.9
|
1.0
|
O6
|
A:G78
|
4.5
|
27.3
|
1.0
|
O5'
|
A:C77
|
4.9
|
28.2
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 5kpy
Go back to
Magnesium Binding Sites List in 5kpy
Magnesium binding site 3 out
of 6 in the Structure of A 5-Hydroxytryptophan Aptamer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg116
b:30.3
occ:1.00
|
O
|
A:HOH252
|
2.5
|
19.6
|
1.0
|
O
|
A:HOH249
|
2.7
|
20.0
|
1.0
|
O
|
A:HOH247
|
2.9
|
19.1
|
0.9
|
O6
|
A:G20
|
3.9
|
19.8
|
1.0
|
OP2
|
A:C18
|
4.6
|
30.3
|
1.0
|
OP2
|
A:A74
|
4.7
|
16.5
|
1.0
|
O4
|
A:U19
|
4.7
|
22.3
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 5kpy
Go back to
Magnesium Binding Sites List in 5kpy
Magnesium binding site 4 out
of 6 in the Structure of A 5-Hydroxytryptophan Aptamer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg117
b:38.3
occ:1.00
|
O2
|
A:C60
|
2.3
|
35.4
|
1.0
|
C2
|
A:A66
|
3.1
|
41.8
|
1.0
|
C2
|
A:U67
|
3.2
|
35.4
|
1.0
|
O2
|
A:U67
|
3.3
|
36.6
|
1.0
|
O4'
|
A:C61
|
3.3
|
39.7
|
1.0
|
O2'
|
A:C60
|
3.3
|
35.3
|
1.0
|
N2
|
A:G38
|
3.3
|
37.1
|
1.0
|
C1'
|
A:C61
|
3.4
|
39.0
|
1.0
|
C2
|
A:C60
|
3.5
|
34.4
|
1.0
|
N1
|
A:A66
|
3.5
|
40.9
|
1.0
|
N1
|
A:U67
|
3.6
|
37.9
|
1.0
|
C2'
|
A:C60
|
3.6
|
36.0
|
1.0
|
N3
|
A:U67
|
3.6
|
33.7
|
1.0
|
N1
|
A:C61
|
3.7
|
37.2
|
1.0
|
C1'
|
A:C60
|
3.8
|
34.2
|
1.0
|
C1'
|
A:U67
|
4.0
|
39.6
|
1.0
|
C6
|
A:C61
|
4.1
|
37.8
|
1.0
|
N3
|
A:A66
|
4.1
|
45.1
|
1.0
|
N1
|
A:C60
|
4.2
|
33.5
|
1.0
|
C6
|
A:U67
|
4.2
|
38.2
|
1.0
|
C4
|
A:U67
|
4.3
|
35.1
|
1.0
|
C2
|
A:C61
|
4.3
|
37.5
|
1.0
|
N3
|
A:C60
|
4.5
|
34.1
|
1.0
|
O2
|
A:C61
|
4.5
|
39.5
|
1.0
|
C5
|
A:U67
|
4.6
|
38.2
|
1.0
|
C2
|
A:G38
|
4.6
|
36.8
|
1.0
|
C4'
|
A:C61
|
4.6
|
40.8
|
1.0
|
O4'
|
A:U67
|
4.7
|
42.3
|
1.0
|
C2'
|
A:C61
|
4.8
|
41.4
|
1.0
|
C6
|
A:A66
|
4.9
|
42.5
|
1.0
|
N1
|
A:A59
|
5.0
|
29.9
|
1.0
|
C5
|
A:C61
|
5.0
|
37.0
|
1.0
|
O2'
|
A:C61
|
5.0
|
43.0
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 5kpy
Go back to
Magnesium Binding Sites List in 5kpy
Magnesium binding site 5 out
of 6 in the Structure of A 5-Hydroxytryptophan Aptamer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg118
b:20.1
occ:1.00
|
O2'
|
A:A48
|
2.7
|
15.7
|
1.0
|
N3
|
A:A48
|
3.0
|
15.7
|
1.0
|
C2'
|
A:A48
|
3.1
|
16.6
|
1.0
|
OP2
|
A:U51
|
3.3
|
19.8
|
1.0
|
C1'
|
A:A48
|
3.4
|
15.9
|
1.0
|
CH2
|
A:4PQ101
|
3.7
|
15.6
|
1.0
|
O
|
A:HOH269
|
3.7
|
17.9
|
0.9
|
C4
|
A:A48
|
3.8
|
16.1
|
1.0
|
C2
|
A:A48
|
3.9
|
16.5
|
1.0
|
O5'
|
A:U51
|
4.0
|
18.5
|
1.0
|
N9
|
A:A48
|
4.0
|
16.0
|
1.0
|
P
|
A:U51
|
4.0
|
21.1
|
1.0
|
CZ3
|
A:4PQ101
|
4.3
|
16.3
|
1.0
|
CZ2
|
A:4PQ101
|
4.3
|
15.9
|
1.0
|
OAD
|
A:4PQ101
|
4.4
|
17.3
|
1.0
|
OP1
|
A:U51
|
4.4
|
17.7
|
1.0
|
O2
|
A:C75
|
4.5
|
18.4
|
1.0
|
C5'
|
A:A49
|
4.5
|
16.6
|
1.0
|
C3'
|
A:A48
|
4.6
|
15.2
|
1.0
|
O4'
|
A:U51
|
4.6
|
19.6
|
1.0
|
O4'
|
A:A48
|
4.7
|
15.4
|
1.0
|
C2
|
A:C75
|
4.9
|
19.2
|
1.0
|
O
|
A:HOH294
|
4.9
|
20.6
|
0.8
|
N2
|
A:G47
|
5.0
|
16.5
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 5kpy
Go back to
Magnesium Binding Sites List in 5kpy
Magnesium binding site 6 out
of 6 in the Structure of A 5-Hydroxytryptophan Aptamer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg119
b:25.6
occ:1.00
|
HN43
|
A:IRI106
|
2.0
|
21.8
|
1.0
|
HN52
|
A:IRI106
|
2.4
|
19.8
|
1.0
|
O
|
A:4PQ101
|
2.6
|
17.6
|
1.0
|
N4
|
A:IRI106
|
2.9
|
18.2
|
1.0
|
N5
|
A:IRI106
|
3.2
|
16.5
|
1.0
|
HN41
|
A:IRI106
|
3.3
|
21.8
|
1.0
|
HN42
|
A:IRI106
|
3.3
|
21.8
|
1.0
|
C
|
A:4PQ101
|
3.4
|
16.6
|
1.0
|
C4'
|
A:U46
|
3.5
|
16.5
|
1.0
|
OXT
|
A:4PQ101
|
3.5
|
16.1
|
1.0
|
HN51
|
A:IRI106
|
3.5
|
19.8
|
1.0
|
O4'
|
A:U46
|
3.6
|
15.4
|
1.0
|
O
|
A:HOH236
|
3.7
|
22.2
|
0.8
|
HN53
|
A:IRI106
|
3.9
|
19.8
|
1.0
|
O2'
|
A:U45
|
3.9
|
18.7
|
1.0
|
C5'
|
A:U46
|
3.9
|
17.7
|
1.0
|
HN31
|
A:IRI106
|
4.0
|
18.7
|
1.0
|
IR
|
A:IRI106
|
4.3
|
17.4
|
1.0
|
C1'
|
A:U46
|
4.5
|
17.0
|
1.0
|
CD1
|
A:4PQ101
|
4.6
|
16.4
|
1.0
|
N3
|
A:IRI106
|
4.6
|
15.6
|
1.0
|
O
|
A:HOH240
|
4.7
|
17.1
|
0.7
|
O2'
|
A:U46
|
4.7
|
16.8
|
1.0
|
C2'
|
A:U45
|
4.7
|
17.0
|
1.0
|
HN13
|
A:IRI106
|
4.7
|
16.6
|
1.0
|
C3'
|
A:U46
|
4.8
|
16.3
|
1.0
|
CA
|
A:4PQ101
|
4.8
|
16.5
|
1.0
|
O2
|
A:U45
|
5.0
|
15.5
|
1.0
|
C2'
|
A:U46
|
5.0
|
15.8
|
1.0
|
|
Reference:
E.B.Porter,
J.T.Polaski,
M.M.Morck,
R.T.Batey.
Recurrent Rna Motifs As Scaffolds For Genetically Encodable Small-Molecule Biosensors. Nat. Chem. Biol. V. 13 295 2017.
ISSN: ESSN 1552-4469
PubMed: 28092358
DOI: 10.1038/NCHEMBIO.2278
Page generated: Sun Sep 29 19:11:17 2024
|