Sodium in PDB 5ndh: The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop
Protein crystallography data
The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh
was solved by
L.Huang,
J.Wang,
D.M.J.Lilley,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.17 /
1.81
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.727,
57.825,
100.862,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.7 /
22.2
|
Other elements in 5ndh:
The structure of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop
(pdb code 5ndh). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 5ndh
Go back to
Sodium Binding Sites List in 5ndh
Sodium binding site 1 out
of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na102
b:73.7
occ:1.00
|
O
|
C:HOH220
|
2.6
|
44.3
|
1.0
|
HO2'
|
A:C8
|
3.4
|
44.1
|
1.0
|
O2'
|
A:C8
|
3.5
|
36.8
|
1.0
|
O4'
|
A:G9
|
3.9
|
37.2
|
1.0
|
H1'
|
A:G9
|
4.3
|
42.4
|
1.0
|
H5'
|
C:C11
|
4.3
|
41.3
|
1.0
|
H4'
|
C:C11
|
4.3
|
48.6
|
1.0
|
H2'
|
A:C8
|
4.4
|
48.0
|
1.0
|
O2
|
A:C8
|
4.4
|
36.7
|
1.0
|
H22
|
C:G9
|
4.4
|
43.0
|
1.0
|
C2'
|
A:C8
|
4.5
|
40.0
|
1.0
|
H5'
|
A:G9
|
4.5
|
44.1
|
1.0
|
O4'
|
C:C11
|
4.5
|
36.7
|
1.0
|
H4'
|
A:G9
|
4.6
|
42.4
|
1.0
|
H21
|
C:G9
|
4.6
|
43.0
|
1.0
|
C1'
|
A:G9
|
4.7
|
35.3
|
1.0
|
O
|
A:HOH210
|
4.7
|
47.7
|
1.0
|
H1'
|
A:C8
|
4.7
|
40.1
|
1.0
|
H62
|
A:A10
|
4.7
|
49.4
|
1.0
|
C4'
|
A:G9
|
4.8
|
35.3
|
1.0
|
O2'
|
C:A10
|
4.8
|
61.5
|
1.0
|
C4'
|
C:C11
|
4.8
|
40.5
|
1.0
|
HO2'
|
C:A10
|
4.9
|
73.7
|
1.0
|
N2
|
C:G9
|
4.9
|
35.9
|
1.0
|
|
Sodium binding site 2 out
of 4 in 5ndh
Go back to
Sodium Binding Sites List in 5ndh
Sodium binding site 2 out
of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na102
b:58.5
occ:1.00
|
O6
|
B:G3
|
2.9
|
32.2
|
1.0
|
O
|
B:HOH208
|
3.3
|
39.3
|
1.0
|
N7
|
B:G3
|
3.4
|
36.4
|
1.0
|
HN42
|
B:CBV2
|
3.5
|
48.3
|
1.0
|
N4
|
B:CBV2
|
3.5
|
40.3
|
1.0
|
O6
|
B:G4
|
3.6
|
33.4
|
1.0
|
HN41
|
B:CBV2
|
3.6
|
48.3
|
1.0
|
C6
|
B:G3
|
3.7
|
32.0
|
1.0
|
C4
|
B:CBV2
|
3.8
|
35.2
|
1.0
|
C5
|
B:G3
|
3.9
|
33.6
|
1.0
|
H42
|
B:C14
|
4.1
|
41.1
|
1.0
|
C5
|
B:CBV2
|
4.3
|
46.3
|
1.0
|
H42
|
B:C13
|
4.4
|
47.4
|
1.0
|
N7
|
B:G4
|
4.4
|
34.8
|
1.0
|
C6
|
B:G4
|
4.4
|
36.2
|
1.0
|
N3
|
B:CBV2
|
4.5
|
34.7
|
1.0
|
BR
|
B:CBV2
|
4.6
|
66.3
|
1.0
|
O6
|
B:G15
|
4.6
|
36.1
|
1.0
|
C8
|
B:G3
|
4.6
|
40.7
|
1.0
|
C5
|
B:G4
|
4.7
|
35.2
|
1.0
|
N4
|
B:C14
|
4.7
|
34.3
|
1.0
|
H41
|
B:C14
|
4.8
|
41.1
|
1.0
|
H41
|
B:C13
|
4.8
|
47.4
|
1.0
|
H1
|
B:G15
|
4.9
|
41.6
|
1.0
|
N4
|
B:C13
|
4.9
|
39.5
|
1.0
|
N1
|
B:G3
|
5.0
|
36.7
|
1.0
|
H8
|
B:G3
|
5.0
|
48.8
|
1.0
|
|
Sodium binding site 3 out
of 4 in 5ndh
Go back to
Sodium Binding Sites List in 5ndh
Sodium binding site 3 out
of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na103
b:63.1
occ:1.00
|
H22
|
B:G1
|
2.7
|
47.8
|
1.0
|
H1'
|
B:CBV2
|
3.2
|
67.3
|
1.0
|
N2
|
B:G1
|
3.5
|
39.9
|
1.0
|
O
|
C:HOH221
|
3.9
|
58.1
|
1.0
|
O4'
|
B:CBV2
|
3.9
|
50.4
|
1.0
|
H21
|
B:G1
|
3.9
|
47.8
|
1.0
|
C1'
|
B:CBV2
|
4.0
|
56.1
|
1.0
|
O
|
C:HOH207
|
4.0
|
50.7
|
1.0
|
HO2'
|
B:CBV2
|
4.2
|
49.3
|
1.0
|
N3
|
B:G1
|
4.5
|
40.7
|
1.0
|
C2
|
B:G1
|
4.5
|
40.6
|
1.0
|
O
|
B:HOH213
|
4.5
|
57.1
|
1.0
|
O2'
|
B:CBV2
|
4.6
|
41.1
|
1.0
|
HO2'
|
B:G1
|
4.6
|
54.1
|
1.0
|
H4'
|
B:CBV2
|
4.6
|
58.8
|
1.0
|
H22
|
C:G1
|
4.7
|
47.4
|
1.0
|
N1
|
B:CBV2
|
4.9
|
36.1
|
1.0
|
C4'
|
B:CBV2
|
4.9
|
49.0
|
1.0
|
C2'
|
B:CBV2
|
5.0
|
64.0
|
1.0
|
O2
|
B:CBV2
|
5.0
|
34.9
|
1.0
|
|
Sodium binding site 4 out
of 4 in 5ndh
Go back to
Sodium Binding Sites List in 5ndh
Sodium binding site 4 out
of 4 in the The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na102
b:59.4
occ:1.00
|
O2'
|
C:C8
|
3.1
|
40.7
|
1.0
|
O2
|
C:C8
|
3.1
|
45.1
|
1.0
|
HO2'
|
C:C8
|
3.3
|
48.8
|
1.0
|
H4'
|
A:C11
|
3.3
|
49.4
|
1.0
|
H1'
|
C:C8
|
3.5
|
57.8
|
1.0
|
O4'
|
A:C11
|
3.5
|
41.7
|
1.0
|
H21
|
A:G9
|
3.7
|
48.0
|
1.0
|
H5'
|
A:C11
|
3.7
|
54.6
|
1.0
|
H2'
|
C:C8
|
3.7
|
64.1
|
1.0
|
C2'
|
C:C8
|
3.8
|
53.4
|
1.0
|
C4'
|
A:C11
|
3.8
|
41.2
|
1.0
|
H22
|
A:G9
|
3.9
|
48.0
|
1.0
|
O4'
|
C:G9
|
4.0
|
45.6
|
1.0
|
C1'
|
C:C8
|
4.1
|
48.2
|
1.0
|
N2
|
A:G9
|
4.2
|
40.0
|
1.0
|
H1'
|
A:C11
|
4.3
|
44.0
|
1.0
|
C5'
|
A:C11
|
4.3
|
45.5
|
1.0
|
H1'
|
C:G9
|
4.3
|
51.5
|
1.0
|
C2
|
C:C8
|
4.3
|
45.0
|
1.0
|
C1'
|
A:C11
|
4.5
|
36.7
|
1.0
|
HO2'
|
A:A10
|
4.5
|
63.4
|
1.0
|
O2'
|
A:A10
|
4.5
|
52.9
|
1.0
|
H5''
|
A:C11
|
4.6
|
54.6
|
1.0
|
C1'
|
C:G9
|
4.7
|
42.9
|
1.0
|
N1
|
C:C8
|
4.7
|
45.8
|
1.0
|
H5'
|
C:G9
|
4.8
|
53.4
|
1.0
|
H4'
|
C:G9
|
4.9
|
47.1
|
1.0
|
O2'
|
A:C11
|
4.9
|
43.5
|
1.0
|
C4'
|
C:G9
|
5.0
|
39.2
|
1.0
|
|
Reference:
L.Huang,
J.Wang,
D.M.J.Lilley.
The Structure of the Guanidine-II Riboswitch. Cell Chem Biol V. 24 695 2017.
ISSN: ESSN 2451-9456
PubMed: 28529131
DOI: 10.1016/J.CHEMBIOL.2017.05.014
Page generated: Mon Oct 7 22:55:51 2024
|