Potassium in PDB 4b5r: Sam-I Riboswitch Bearing the H. Marismortui K-T-7
Protein crystallography data
The structure of Sam-I Riboswitch Bearing the H. Marismortui K-T-7, PDB code: 4b5r
was solved by
P.Daldrop,
D.M.J.Lilley,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
54.90 /
2.95
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.720,
58.720,
154.710,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.913 /
25.195
|
Other elements in 4b5r:
The structure of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
(pdb code 4b5r). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the
Sam-I Riboswitch Bearing the H. Marismortui K-T-7, PDB code: 4b5r:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
Potassium binding site 1 out
of 7 in 4b5r
Go back to
Potassium Binding Sites List in 4b5r
Potassium binding site 1 out
of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1097
b:48.8
occ:1.00
|
OP2
|
A:G11
|
2.7
|
35.9
|
1.0
|
OP1
|
A:A62
|
2.7
|
36.8
|
1.0
|
OP2
|
A:A10
|
3.5
|
39.3
|
1.0
|
P
|
A:G11
|
4.1
|
35.8
|
1.0
|
P
|
A:A62
|
4.2
|
37.6
|
1.0
|
O5'
|
A:A62
|
4.5
|
36.1
|
1.0
|
C5'
|
A:A62
|
4.6
|
34.4
|
1.0
|
O5'
|
A:G11
|
4.6
|
34.6
|
1.0
|
P
|
A:A10
|
4.7
|
37.3
|
1.0
|
OP1
|
A:G11
|
4.7
|
37.2
|
1.0
|
N7
|
A:G11
|
4.9
|
28.9
|
1.0
|
O5'
|
A:A10
|
4.9
|
35.8
|
1.0
|
C8
|
A:G11
|
5.0
|
28.8
|
1.0
|
O3'
|
A:A61
|
5.0
|
32.4
|
1.0
|
|
Potassium binding site 2 out
of 7 in 4b5r
Go back to
Potassium Binding Sites List in 4b5r
Potassium binding site 2 out
of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1098
b:48.1
occ:1.00
|
O6
|
A:G50
|
2.9
|
87.7
|
1.0
|
C6
|
A:G50
|
3.7
|
84.0
|
1.0
|
N1
|
A:G50
|
4.0
|
80.8
|
1.0
|
OP1
|
A:A52
|
4.1
|
63.0
|
1.0
|
C5
|
A:G50
|
5.0
|
82.7
|
1.0
|
|
Potassium binding site 3 out
of 7 in 4b5r
Go back to
Potassium Binding Sites List in 4b5r
Potassium binding site 3 out
of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1100
b:38.9
occ:1.00
|
O6
|
A:G82
|
3.0
|
27.2
|
1.0
|
O4
|
A:U81
|
3.6
|
24.5
|
1.0
|
OP1
|
A:U67
|
3.9
|
26.0
|
1.0
|
C6
|
A:G82
|
4.0
|
26.0
|
1.0
|
C4
|
A:U81
|
4.2
|
25.6
|
1.0
|
N6
|
A:A83
|
4.3
|
28.6
|
1.0
|
N4
|
A:C69
|
4.3
|
24.8
|
1.0
|
N7
|
A:G82
|
4.3
|
25.4
|
1.0
|
C5
|
A:G82
|
4.6
|
25.4
|
1.0
|
C5
|
A:U81
|
4.6
|
26.0
|
1.0
|
OP2
|
A:G68
|
4.7
|
27.6
|
1.0
|
P
|
A:U67
|
4.9
|
25.6
|
1.0
|
|
Potassium binding site 4 out
of 7 in 4b5r
Go back to
Potassium Binding Sites List in 4b5r
Potassium binding site 4 out
of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1102
b:37.0
occ:1.00
|
O6
|
A:G79
|
2.7
|
33.1
|
1.0
|
O4
|
A:U80
|
3.2
|
33.8
|
1.0
|
O6
|
A:G71
|
3.2
|
32.6
|
1.0
|
N6
|
A:A70
|
3.5
|
25.6
|
1.0
|
C6
|
A:G79
|
3.8
|
33.3
|
1.0
|
N4
|
A:C72
|
4.1
|
25.2
|
1.0
|
C4
|
A:U80
|
4.1
|
33.6
|
1.0
|
N3
|
A:U80
|
4.2
|
33.4
|
1.0
|
C6
|
A:G71
|
4.4
|
31.5
|
1.0
|
C6
|
A:A70
|
4.5
|
26.3
|
1.0
|
N7
|
A:G79
|
4.5
|
32.2
|
1.0
|
C5
|
A:G79
|
4.5
|
31.8
|
1.0
|
N7
|
A:A70
|
4.8
|
26.6
|
1.0
|
N1
|
A:G79
|
4.9
|
33.9
|
1.0
|
OP1
|
A:G68
|
4.9
|
28.6
|
1.0
|
C5
|
A:A70
|
4.9
|
26.8
|
1.0
|
N7
|
A:G71
|
5.0
|
31.1
|
1.0
|
|
Potassium binding site 5 out
of 7 in 4b5r
Go back to
Potassium Binding Sites List in 4b5r
Potassium binding site 5 out
of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1103
b:26.3
occ:1.00
|
O6
|
A:G86
|
3.4
|
30.2
|
1.0
|
N7
|
A:G86
|
3.5
|
28.8
|
1.0
|
N7
|
A:A85
|
3.5
|
29.5
|
1.0
|
C6
|
A:G86
|
4.1
|
28.0
|
1.0
|
C5
|
A:G86
|
4.1
|
28.1
|
1.0
|
C8
|
A:A85
|
4.2
|
29.6
|
1.0
|
OP2
|
A:A85
|
4.3
|
30.0
|
1.0
|
C5
|
A:A85
|
4.5
|
29.2
|
1.0
|
N6
|
A:A85
|
4.6
|
30.2
|
1.0
|
C8
|
A:G86
|
4.6
|
27.8
|
1.0
|
N6
|
A:A87
|
4.6
|
28.1
|
1.0
|
OP2
|
A:A84
|
4.9
|
29.6
|
1.0
|
C6
|
A:A85
|
4.9
|
30.5
|
1.0
|
|
Potassium binding site 6 out
of 7 in 4b5r
Go back to
Potassium Binding Sites List in 4b5r
Potassium binding site 6 out
of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1113
b:42.2
occ:1.00
|
N7
|
A:G56
|
3.3
|
72.4
|
1.0
|
O6
|
A:G56
|
3.5
|
69.0
|
1.0
|
N1
|
A:A45
|
3.7
|
38.9
|
1.0
|
C5
|
A:G56
|
4.1
|
71.2
|
1.0
|
N6
|
A:A45
|
4.1
|
38.1
|
1.0
|
C6
|
A:G56
|
4.2
|
68.2
|
1.0
|
C8
|
A:G56
|
4.4
|
71.9
|
1.0
|
C6
|
A:A45
|
4.4
|
38.4
|
1.0
|
OP2
|
A:G56
|
4.4
|
70.8
|
1.0
|
C2
|
A:A45
|
4.7
|
38.9
|
1.0
|
OP2
|
A:G55
|
4.8
|
56.9
|
1.0
|
N4
|
A:C44
|
4.9
|
32.5
|
1.0
|
N7
|
A:G55
|
4.9
|
70.5
|
1.0
|
|
Potassium binding site 7 out
of 7 in 4b5r
Go back to
Potassium Binding Sites List in 4b5r
Potassium binding site 7 out
of 7 in the Sam-I Riboswitch Bearing the H. Marismortui K-T-7
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Sam-I Riboswitch Bearing the H. Marismortui K-T-7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1114
b:37.0
occ:1.00
|
N7
|
A:G13
|
3.0
|
44.2
|
1.0
|
C8
|
A:G13
|
3.6
|
45.9
|
1.0
|
OP2
|
A:A61
|
3.9
|
25.7
|
1.0
|
C5
|
A:G13
|
4.2
|
45.5
|
1.0
|
C2'
|
A:C60
|
4.4
|
25.1
|
1.0
|
O2
|
A:C60
|
4.6
|
23.8
|
1.0
|
O6
|
A:G13
|
4.7
|
44.6
|
1.0
|
C2
|
A:C60
|
4.9
|
24.5
|
1.0
|
C6
|
A:G13
|
4.9
|
45.2
|
1.0
|
O2'
|
A:C60
|
4.9
|
26.2
|
1.0
|
N9
|
A:G13
|
4.9
|
47.5
|
1.0
|
|
Reference:
P.Daldrop,
D.M.J.Lilley.
The Plasticity of A Structural Motif in Rna: Structural Polymorphism of A Kink Turn As A Function of Its Environment. Rna V. 19 357 2013.
ISSN: ISSN 1355-8382
PubMed: 23325110
DOI: 10.1261/RNA.036657.112
Page generated: Mon Aug 12 10:06:06 2024
|