Bromine 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:
Bromine Binding Sites:
The binding sites of Bromine 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 Bromine atom.
In total 4 binding sites of Bromine where determined in the
The Structure of the G. Violaceus Guanidine II Riboswitch P2 Stem-Loop, PDB code: 5ndh:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 5ndh
Go back to
Bromine Binding Sites List in 5ndh
Bromine 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 Bromine with other atoms in the Br 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:Br2
b:53.7
occ:1.00
|
BR
|
A:CBV2
|
0.0
|
53.7
|
1.0
|
C5
|
A:CBV2
|
1.9
|
46.0
|
1.0
|
HN42
|
A:CBV2
|
2.7
|
52.5
|
1.0
|
C4
|
A:CBV2
|
2.9
|
45.0
|
1.0
|
C6
|
A:CBV2
|
3.0
|
43.0
|
1.0
|
H6
|
A:CBV2
|
3.1
|
51.6
|
1.0
|
N4
|
A:CBV2
|
3.1
|
43.8
|
1.0
|
H3'
|
A:G1
|
3.3
|
1.0
|
1.0
|
O
|
A:HOH202
|
3.3
|
56.4
|
1.0
|
O2P
|
A:CBV2
|
3.5
|
45.9
|
1.0
|
N7
|
A:G1
|
3.6
|
47.2
|
1.0
|
C5
|
A:G1
|
3.7
|
46.7
|
1.0
|
C8
|
A:G1
|
3.7
|
49.9
|
1.0
|
H2'
|
A:G1
|
3.9
|
79.3
|
1.0
|
C4
|
A:G1
|
3.9
|
47.5
|
1.0
|
N9
|
A:G1
|
4.0
|
48.5
|
1.0
|
HN41
|
A:CBV2
|
4.0
|
52.5
|
1.0
|
H8
|
A:G1
|
4.1
|
59.9
|
1.0
|
C3'
|
A:G1
|
4.2
|
95.8
|
1.0
|
C6
|
A:G1
|
4.2
|
38.6
|
1.0
|
N3
|
A:CBV2
|
4.3
|
39.8
|
1.0
|
N1
|
A:CBV2
|
4.3
|
47.8
|
1.0
|
O5'
|
A:G1
|
4.3
|
54.3
|
1.0
|
C2'
|
A:G1
|
4.4
|
66.1
|
1.0
|
O5'
|
A:CBV2
|
4.5
|
60.1
|
1.0
|
P
|
A:CBV2
|
4.5
|
59.3
|
1.0
|
N3
|
A:G1
|
4.6
|
42.2
|
1.0
|
O6
|
A:G1
|
4.7
|
39.4
|
1.0
|
N7
|
A:G3
|
4.7
|
37.3
|
1.0
|
C1'
|
A:G1
|
4.8
|
62.4
|
1.0
|
N1
|
A:G1
|
4.8
|
38.1
|
1.0
|
O3'
|
A:G1
|
4.8
|
81.5
|
1.0
|
C2
|
A:CBV2
|
4.9
|
44.0
|
1.0
|
|
Bromine binding site 2 out
of 4 in 5ndh
Go back to
Bromine Binding Sites List in 5ndh
Bromine 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 Bromine with other atoms in the Br 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:Br2
b:66.3
occ:1.00
|
BR
|
B:CBV2
|
0.0
|
66.3
|
1.0
|
C5
|
B:CBV2
|
1.9
|
46.3
|
1.0
|
HN42
|
B:CBV2
|
2.8
|
48.3
|
1.0
|
C6
|
B:CBV2
|
2.9
|
36.8
|
1.0
|
C4
|
B:CBV2
|
3.0
|
35.2
|
1.0
|
H6
|
B:CBV2
|
3.0
|
44.1
|
1.0
|
N4
|
B:CBV2
|
3.2
|
40.3
|
1.0
|
H3'
|
B:G1
|
3.4
|
69.3
|
1.0
|
HO5'
|
B:G1
|
3.5
|
64.9
|
1.0
|
N7
|
B:G1
|
3.5
|
52.5
|
1.0
|
C5
|
B:G1
|
3.7
|
46.1
|
1.0
|
C8
|
B:G1
|
3.7
|
50.3
|
1.0
|
O1P
|
B:CBV2
|
3.7
|
40.1
|
1.0
|
C4
|
B:G1
|
4.0
|
45.0
|
1.0
|
N9
|
B:G1
|
4.0
|
48.8
|
1.0
|
H2'
|
B:G1
|
4.0
|
66.8
|
1.0
|
H8
|
B:G1
|
4.1
|
60.4
|
1.0
|
HN41
|
B:CBV2
|
4.1
|
48.3
|
1.0
|
C6
|
B:G1
|
4.2
|
45.6
|
1.0
|
O5'
|
B:G1
|
4.3
|
54.1
|
1.0
|
C3'
|
B:G1
|
4.3
|
57.7
|
1.0
|
N1
|
B:CBV2
|
4.3
|
36.1
|
1.0
|
N3
|
B:CBV2
|
4.3
|
34.7
|
1.0
|
C2'
|
B:G1
|
4.5
|
55.6
|
1.0
|
O5'
|
B:CBV2
|
4.6
|
40.2
|
1.0
|
NA
|
B:NA102
|
4.6
|
58.5
|
1.0
|
O6
|
B:G1
|
4.7
|
40.0
|
1.0
|
N3
|
B:G1
|
4.7
|
40.7
|
1.0
|
P
|
B:CBV2
|
4.7
|
56.4
|
1.0
|
C1'
|
B:G1
|
4.8
|
58.1
|
1.0
|
C2
|
B:CBV2
|
4.8
|
38.6
|
1.0
|
N1
|
B:G1
|
4.9
|
40.0
|
1.0
|
|
Bromine binding site 3 out
of 4 in 5ndh
Go back to
Bromine Binding Sites List in 5ndh
Bromine 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 Bromine with other atoms in the Br 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
|
C:Br2
b:43.0
occ:1.00
|
BR
|
C:CBV2
|
0.0
|
43.0
|
1.0
|
C5
|
C:CBV2
|
1.9
|
41.0
|
1.0
|
HN42
|
C:CBV2
|
2.8
|
47.5
|
1.0
|
C4
|
C:CBV2
|
2.9
|
37.9
|
1.0
|
C6
|
C:CBV2
|
3.0
|
36.2
|
1.0
|
H6
|
C:CBV2
|
3.0
|
43.4
|
1.0
|
N4
|
C:CBV2
|
3.2
|
39.6
|
1.0
|
H3'
|
C:G1
|
3.5
|
64.7
|
1.0
|
O3P
|
C:CBV2
|
3.5
|
68.5
|
1.0
|
N7
|
C:G1
|
3.6
|
43.6
|
1.0
|
C5
|
C:G1
|
3.7
|
43.3
|
1.0
|
C8
|
C:G1
|
3.8
|
41.8
|
1.0
|
O
|
C:HOH212
|
3.9
|
50.0
|
1.0
|
H2'
|
C:G1
|
3.9
|
59.5
|
1.0
|
C4
|
C:G1
|
4.0
|
41.2
|
1.0
|
N9
|
C:G1
|
4.0
|
44.3
|
1.0
|
HN41
|
C:CBV2
|
4.0
|
47.5
|
1.0
|
O
|
C:HOH201
|
4.1
|
51.7
|
1.0
|
H8
|
C:G1
|
4.2
|
50.2
|
1.0
|
C6
|
C:G1
|
4.3
|
44.7
|
1.0
|
N3
|
C:CBV2
|
4.3
|
37.4
|
1.0
|
N1
|
C:CBV2
|
4.3
|
36.4
|
1.0
|
C3'
|
C:G1
|
4.3
|
53.9
|
1.0
|
O5'
|
C:CBV2
|
4.4
|
44.5
|
1.0
|
P
|
C:CBV2
|
4.5
|
49.3
|
1.0
|
C2'
|
C:G1
|
4.5
|
49.6
|
1.0
|
O5'
|
C:G1
|
4.7
|
46.6
|
1.0
|
N3
|
C:G1
|
4.7
|
43.6
|
1.0
|
O6
|
C:G1
|
4.7
|
43.6
|
1.0
|
O2P
|
C:CBV2
|
4.7
|
80.1
|
1.0
|
C2
|
C:CBV2
|
4.8
|
41.2
|
1.0
|
N1
|
C:G1
|
4.9
|
41.4
|
1.0
|
C1'
|
C:G1
|
4.9
|
49.0
|
1.0
|
O3'
|
C:G1
|
4.9
|
56.3
|
1.0
|
|
Bromine binding site 4 out
of 4 in 5ndh
Go back to
Bromine Binding Sites List in 5ndh
Bromine 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 Bromine with other atoms in the Br 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
|
D:Br2
b:47.5
occ:1.00
|
BR
|
D:CBV2
|
0.0
|
47.5
|
1.0
|
C5
|
D:CBV2
|
1.9
|
43.8
|
1.0
|
HN42
|
D:CBV2
|
2.7
|
50.4
|
1.0
|
C4
|
D:CBV2
|
2.9
|
34.7
|
1.0
|
C6
|
D:CBV2
|
2.9
|
43.2
|
1.0
|
H6
|
D:CBV2
|
3.0
|
51.9
|
1.0
|
N4
|
D:CBV2
|
3.2
|
42.0
|
1.0
|
H3'
|
D:G1
|
3.3
|
63.7
|
1.0
|
O1P
|
D:CBV2
|
3.5
|
56.0
|
1.0
|
HO5'
|
D:G1
|
3.5
|
66.4
|
1.0
|
N7
|
D:G1
|
3.6
|
40.2
|
1.0
|
C5
|
D:G1
|
3.7
|
38.0
|
1.0
|
C8
|
D:G1
|
3.8
|
37.8
|
1.0
|
C4
|
D:G1
|
4.0
|
41.9
|
1.0
|
N9
|
D:G1
|
4.0
|
41.6
|
1.0
|
O2P
|
D:CBV2
|
4.0
|
49.4
|
1.0
|
HN41
|
D:CBV2
|
4.0
|
50.4
|
1.0
|
H2'
|
D:G1
|
4.0
|
61.4
|
1.0
|
H8
|
D:G1
|
4.2
|
45.4
|
1.0
|
C3'
|
D:G1
|
4.2
|
53.1
|
1.0
|
N3
|
D:CBV2
|
4.3
|
35.2
|
1.0
|
O
|
D:HOH208
|
4.3
|
54.7
|
1.0
|
C6
|
D:G1
|
4.3
|
45.7
|
1.0
|
N1
|
D:CBV2
|
4.3
|
40.0
|
1.0
|
O5'
|
D:G1
|
4.3
|
55.3
|
1.0
|
O5'
|
D:CBV2
|
4.5
|
43.3
|
1.0
|
C2'
|
D:G1
|
4.6
|
51.1
|
1.0
|
P
|
D:CBV2
|
4.6
|
46.6
|
1.0
|
N3
|
D:G1
|
4.7
|
43.6
|
1.0
|
O6
|
D:G1
|
4.7
|
39.3
|
1.0
|
C2
|
D:CBV2
|
4.8
|
36.5
|
1.0
|
C1'
|
D:G1
|
4.9
|
45.7
|
1.0
|
N1
|
D:G1
|
4.9
|
47.2
|
1.0
|
O3'
|
D:G1
|
4.9
|
58.0
|
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: Thu Jul 11 00:27:40 2024
|