Bromine in PDB 5nz3: The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine
Protein crystallography data
The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine, PDB code: 5nz3
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)
|
48.78 /
2.06
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.491,
83.491,
66.071,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.9 /
27.4
|
Other elements in 5nz3:
The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine also contains other interesting chemical elements:
Bromine Binding Sites:
The binding sites of Bromine atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine
(pdb code 5nz3). 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 Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine, PDB code: 5nz3:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 5nz3
Go back to
Bromine Binding Sites List in 5nz3
Bromine binding site 1 out
of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine
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 Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br2
b:70.7
occ:1.00
|
BR
|
A:CBV2
|
0.0
|
70.7
|
1.0
|
C5
|
A:CBV2
|
1.9
|
57.6
|
1.0
|
HN41
|
A:CBV2
|
2.8
|
68.6
|
1.0
|
H3'
|
A:C1
|
2.9
|
0.4
|
1.0
|
C6
|
A:CBV2
|
3.0
|
58.9
|
1.0
|
C4
|
A:CBV2
|
3.0
|
56.5
|
1.0
|
H6
|
A:CBV2
|
3.0
|
70.6
|
1.0
|
N4
|
A:CBV2
|
3.2
|
57.2
|
1.0
|
O2P
|
A:CBV2
|
3.3
|
67.0
|
1.0
|
C6
|
A:C1
|
3.5
|
87.7
|
1.0
|
C5
|
A:C1
|
3.6
|
75.8
|
1.0
|
O5'
|
A:C1
|
3.7
|
0.1
|
1.0
|
O
|
A:HOH213
|
3.7
|
56.4
|
1.0
|
H6
|
A:C1
|
3.8
|
0.2
|
1.0
|
H5
|
A:C1
|
3.8
|
90.9
|
1.0
|
C3'
|
A:C1
|
3.8
|
1.0
|
1.0
|
N1
|
A:C1
|
3.9
|
93.8
|
1.0
|
C4
|
A:C1
|
3.9
|
70.8
|
1.0
|
HO5'
|
A:C1
|
4.0
|
0.5
|
1.0
|
H2'
|
A:C1
|
4.0
|
0.9
|
1.0
|
HN42
|
A:CBV2
|
4.1
|
68.6
|
1.0
|
N3
|
A:C1
|
4.2
|
69.7
|
1.0
|
C2
|
A:C1
|
4.2
|
79.5
|
1.0
|
N3
|
A:CBV2
|
4.3
|
54.1
|
1.0
|
N1
|
A:CBV2
|
4.3
|
59.4
|
1.0
|
O5'
|
A:CBV2
|
4.3
|
63.1
|
1.0
|
P
|
A:CBV2
|
4.4
|
68.9
|
1.0
|
C2'
|
A:C1
|
4.4
|
0.4
|
1.0
|
N4
|
A:C1
|
4.6
|
64.4
|
1.0
|
O3'
|
A:C1
|
4.6
|
94.7
|
1.0
|
C1'
|
A:C1
|
4.6
|
0.2
|
1.0
|
C4'
|
A:C1
|
4.7
|
0.3
|
1.0
|
C5'
|
A:C1
|
4.7
|
0.7
|
1.0
|
H41
|
A:C1
|
4.7
|
77.3
|
1.0
|
MG
|
A:MG104
|
4.7
|
30.0
|
1.0
|
C2
|
A:CBV2
|
4.8
|
54.0
|
1.0
|
O4'
|
A:C1
|
4.8
|
0.3
|
1.0
|
O3P
|
A:CBV2
|
4.9
|
77.2
|
1.0
|
|
Bromine binding site 2 out
of 4 in 5nz3
Go back to
Bromine Binding Sites List in 5nz3
Bromine binding site 2 out
of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine
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 Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br39
b:39.4
occ:1.00
|
BR
|
A:CBV39
|
0.0
|
39.4
|
1.0
|
C5
|
A:CBV39
|
1.9
|
42.5
|
1.0
|
HN42
|
A:CBV39
|
2.9
|
75.1
|
1.0
|
C6
|
A:CBV39
|
2.9
|
45.1
|
1.0
|
H6
|
A:CBV39
|
3.0
|
54.1
|
1.0
|
C4
|
A:CBV39
|
3.0
|
35.2
|
1.0
|
N4
|
A:CBV39
|
3.3
|
62.6
|
1.0
|
N7
|
A:G38
|
3.5
|
34.6
|
1.0
|
H3'
|
A:G38
|
3.6
|
60.4
|
1.0
|
C5
|
A:G38
|
3.6
|
40.0
|
1.0
|
O2P
|
A:CBV39
|
3.7
|
39.3
|
1.0
|
C8
|
A:G38
|
3.7
|
36.5
|
1.0
|
O4
|
A:U11
|
3.8
|
34.1
|
1.0
|
C4
|
A:G38
|
4.0
|
36.3
|
1.0
|
H21
|
A:G10
|
4.0
|
45.8
|
1.0
|
N9
|
A:G38
|
4.0
|
35.8
|
1.0
|
H8
|
A:G38
|
4.1
|
43.9
|
1.0
|
C6
|
A:G38
|
4.1
|
34.6
|
1.0
|
HN41
|
A:CBV39
|
4.2
|
75.1
|
1.0
|
N1
|
A:CBV39
|
4.2
|
36.9
|
1.0
|
NA
|
A:NA106
|
4.3
|
65.2
|
1.0
|
N3
|
A:CBV39
|
4.3
|
39.6
|
1.0
|
H2'
|
A:G38
|
4.3
|
56.0
|
1.0
|
N2
|
A:G10
|
4.4
|
38.2
|
1.0
|
C3'
|
A:G38
|
4.5
|
50.3
|
1.0
|
O6
|
A:G38
|
4.5
|
47.0
|
1.0
|
H1
|
A:G10
|
4.6
|
54.6
|
1.0
|
O5'
|
A:CBV39
|
4.6
|
33.0
|
1.0
|
H22
|
A:G10
|
4.7
|
45.8
|
1.0
|
N3
|
A:G38
|
4.8
|
40.1
|
1.0
|
C2'
|
A:G38
|
4.8
|
46.6
|
1.0
|
N1
|
A:G38
|
4.8
|
42.0
|
1.0
|
C2
|
A:CBV39
|
4.8
|
34.0
|
1.0
|
P
|
A:CBV39
|
4.8
|
40.0
|
1.0
|
C2
|
A:G10
|
4.9
|
41.8
|
1.0
|
N1
|
A:G10
|
4.9
|
45.5
|
1.0
|
C1'
|
A:G38
|
5.0
|
38.4
|
1.0
|
O5'
|
A:G38
|
5.0
|
43.1
|
1.0
|
|
Bromine binding site 3 out
of 4 in 5nz3
Go back to
Bromine Binding Sites List in 5nz3
Bromine binding site 3 out
of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine
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 Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br2
b:99.0
occ:1.00
|
BR
|
B:CBV2
|
0.0
|
99.0
|
1.0
|
C5
|
B:CBV2
|
1.9
|
99.4
|
1.0
|
HN41
|
B:CBV2
|
2.8
|
0.2
|
1.0
|
C4
|
B:CBV2
|
3.0
|
0.3
|
1.0
|
C6
|
B:CBV2
|
3.0
|
97.4
|
1.0
|
H3'
|
B:C1
|
3.0
|
0.3
|
1.0
|
H6
|
B:CBV2
|
3.1
|
0.9
|
1.0
|
N4
|
B:CBV2
|
3.2
|
0.1
|
1.0
|
C5
|
B:C1
|
3.5
|
89.3
|
1.0
|
O1P
|
B:CBV2
|
3.6
|
0.6
|
1.0
|
C6
|
B:C1
|
3.6
|
1.0
|
1.0
|
C4
|
B:C1
|
3.7
|
87.9
|
1.0
|
N1
|
B:C1
|
3.8
|
0.4
|
1.0
|
H5
|
B:C1
|
3.8
|
0.2
|
1.0
|
H6
|
B:C1
|
3.9
|
0.4
|
1.0
|
C3'
|
B:C1
|
3.9
|
0.9
|
1.0
|
H2'
|
B:C1
|
3.9
|
0.9
|
1.0
|
N3
|
B:C1
|
3.9
|
99.1
|
1.0
|
C2
|
B:C1
|
4.0
|
0.1
|
1.0
|
O5'
|
B:C1
|
4.0
|
0.0
|
1.0
|
HN42
|
B:CBV2
|
4.1
|
0.2
|
1.0
|
N3
|
B:CBV2
|
4.3
|
0.2
|
1.0
|
HO5'
|
B:C1
|
4.3
|
0.4
|
1.0
|
N4
|
B:C1
|
4.3
|
88.7
|
1.0
|
N1
|
B:CBV2
|
4.3
|
98.0
|
1.0
|
C2'
|
B:C1
|
4.3
|
0.6
|
1.0
|
P
|
B:CBV2
|
4.5
|
0.7
|
1.0
|
H41
|
B:C1
|
4.6
|
0.5
|
1.0
|
C1'
|
B:C1
|
4.6
|
0.2
|
1.0
|
O5'
|
B:CBV2
|
4.6
|
96.6
|
1.0
|
H5'2
|
B:CBV2
|
4.7
|
0.4
|
1.0
|
O3'
|
B:C1
|
4.7
|
0.2
|
1.0
|
O2
|
B:C1
|
4.7
|
0.2
|
1.0
|
H42
|
B:C1
|
4.8
|
0.5
|
1.0
|
C4'
|
B:C1
|
4.8
|
0.3
|
1.0
|
C2
|
B:CBV2
|
4.9
|
99.9
|
1.0
|
O4'
|
B:C1
|
4.9
|
0.3
|
1.0
|
O3P
|
B:CBV2
|
4.9
|
0.6
|
1.0
|
C5'
|
B:C1
|
5.0
|
0.9
|
1.0
|
|
Bromine binding site 4 out
of 4 in 5nz3
Go back to
Bromine Binding Sites List in 5nz3
Bromine binding site 4 out
of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine
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 Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br39
b:63.2
occ:1.00
|
BR
|
B:CBV39
|
0.0
|
63.2
|
1.0
|
C5
|
B:CBV39
|
1.9
|
53.1
|
1.0
|
HN42
|
B:CBV39
|
2.6
|
66.5
|
1.0
|
C4
|
B:CBV39
|
2.9
|
54.1
|
1.0
|
C6
|
B:CBV39
|
3.0
|
53.6
|
1.0
|
N4
|
B:CBV39
|
3.1
|
55.4
|
1.0
|
H6
|
B:CBV39
|
3.1
|
64.3
|
1.0
|
N7
|
B:G38
|
3.5
|
60.6
|
1.0
|
H3'
|
B:G38
|
3.6
|
82.0
|
1.0
|
C5
|
B:G38
|
3.6
|
69.3
|
1.0
|
C8
|
B:G38
|
3.8
|
62.4
|
1.0
|
O1P
|
B:CBV39
|
3.8
|
47.7
|
1.0
|
O4
|
B:U11
|
3.9
|
59.3
|
1.0
|
HN41
|
B:CBV39
|
3.9
|
66.5
|
1.0
|
C4
|
B:G38
|
4.0
|
64.9
|
1.0
|
N9
|
B:G38
|
4.1
|
69.9
|
1.0
|
C6
|
B:G38
|
4.1
|
66.5
|
1.0
|
H2'
|
B:G38
|
4.1
|
85.1
|
1.0
|
H21
|
B:G10
|
4.1
|
79.9
|
1.0
|
H8
|
B:G38
|
4.1
|
74.8
|
1.0
|
N3
|
B:CBV39
|
4.2
|
54.8
|
1.0
|
N1
|
B:CBV39
|
4.3
|
69.3
|
1.0
|
C3'
|
B:G38
|
4.5
|
68.3
|
1.0
|
O6
|
B:G38
|
4.5
|
74.2
|
1.0
|
MG
|
B:MG101
|
4.5
|
30.0
|
1.0
|
N2
|
B:G10
|
4.5
|
66.6
|
1.0
|
O5'
|
B:CBV39
|
4.5
|
55.3
|
1.0
|
H1
|
B:G10
|
4.7
|
84.2
|
1.0
|
C2'
|
B:G38
|
4.7
|
70.9
|
1.0
|
P
|
B:CBV39
|
4.7
|
55.5
|
1.0
|
N3
|
B:G38
|
4.8
|
63.6
|
1.0
|
N1
|
B:G38
|
4.8
|
76.5
|
1.0
|
C2
|
B:CBV39
|
4.8
|
61.1
|
1.0
|
H22
|
B:G10
|
4.8
|
79.9
|
1.0
|
C1'
|
B:G38
|
5.0
|
73.8
|
1.0
|
|
Reference:
L.Huang,
J.Wang,
T.J.Wilson,
D.M.J.Lilley.
Structure of the Guanidine III Riboswitch. Cell Chem Biol V. 24 1407 2017.
ISSN: ESSN 2451-9456
PubMed: 28988949
DOI: 10.1016/J.CHEMBIOL.2017.08.021
Page generated: Thu Jul 11 00:31:44 2024
|