Bromine in PDB 6qn3: Structure of the Glutamine II Riboswitch
Protein crystallography data
The structure of Structure of the Glutamine II Riboswitch, PDB code: 6qn3
was solved by
L.Huang,
D.M.J.Lilley,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.00 /
2.30
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.502,
115.725,
80.582,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.2 /
29.4
|
Other elements in 6qn3:
The structure of Structure of the Glutamine II Riboswitch also contains other interesting chemical elements:
Bromine Binding Sites:
The binding sites of Bromine atom in the Structure of the Glutamine II Riboswitch
(pdb code 6qn3). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the
Structure of the Glutamine II Riboswitch, PDB code: 6qn3:
Jump to Bromine binding site number:
1;
2;
3;
4;
Bromine binding site 1 out
of 4 in 6qn3
Go back to
Bromine Binding Sites List in 6qn3
Bromine binding site 1 out
of 4 in the Structure of the Glutamine II Riboswitch
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Structure of the Glutamine II Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br102
b:83.9
occ:0.50
|
C5
|
A:C9
|
2.1
|
0.5
|
1.0
|
C4
|
A:C9
|
2.9
|
86.8
|
1.0
|
N4
|
A:C9
|
3.0
|
79.3
|
1.0
|
C6
|
A:C9
|
3.1
|
93.1
|
1.0
|
C5
|
A:C8
|
3.5
|
95.0
|
1.0
|
C4
|
A:C8
|
3.5
|
77.6
|
1.0
|
C6
|
A:C8
|
3.7
|
78.3
|
1.0
|
OP2
|
A:C9
|
3.8
|
94.9
|
1.0
|
N3
|
A:C8
|
3.9
|
72.8
|
1.0
|
N4
|
A:C8
|
4.0
|
72.3
|
1.0
|
N1
|
A:C8
|
4.0
|
89.7
|
1.0
|
C2
|
A:C8
|
4.1
|
89.8
|
1.0
|
N3
|
A:C9
|
4.2
|
86.6
|
1.0
|
N1
|
A:C9
|
4.3
|
81.0
|
1.0
|
BR
|
A:BR103
|
4.4
|
72.8
|
0.5
|
O4
|
A:U10
|
4.5
|
93.7
|
1.0
|
C5
|
A:U10
|
4.6
|
87.1
|
1.0
|
C3'
|
A:C8
|
4.6
|
77.4
|
1.0
|
C2
|
A:C9
|
4.8
|
81.2
|
1.0
|
C2'
|
A:C8
|
4.8
|
90.8
|
1.0
|
O5'
|
A:C9
|
4.8
|
90.0
|
1.0
|
C4
|
A:U10
|
4.9
|
86.6
|
1.0
|
O2
|
A:C8
|
4.9
|
73.5
|
1.0
|
P
|
A:C9
|
4.9
|
0.9
|
1.0
|
C1'
|
A:C8
|
5.0
|
83.2
|
1.0
|
|
Bromine binding site 2 out
of 4 in 6qn3
Go back to
Bromine Binding Sites List in 6qn3
Bromine binding site 2 out
of 4 in the Structure of the Glutamine II Riboswitch
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Structure of the Glutamine II Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Br103
b:72.8
occ:0.50
|
C5
|
A:C8
|
2.1
|
95.0
|
1.0
|
C6
|
A:C8
|
3.1
|
78.3
|
1.0
|
C4
|
A:C8
|
3.1
|
77.6
|
1.0
|
N4
|
A:C8
|
3.2
|
72.3
|
1.0
|
C4
|
A:C7
|
3.5
|
71.0
|
1.0
|
C5
|
A:C7
|
3.5
|
65.5
|
1.0
|
N3
|
A:C7
|
3.7
|
65.8
|
1.0
|
C6
|
A:C7
|
3.7
|
65.5
|
1.0
|
C2
|
A:C7
|
3.9
|
71.4
|
1.0
|
N1
|
A:C7
|
3.9
|
68.5
|
1.0
|
OP2
|
A:C8
|
4.0
|
98.6
|
1.0
|
N4
|
A:C7
|
4.0
|
82.0
|
1.0
|
C3'
|
A:C7
|
4.3
|
69.8
|
1.0
|
N1
|
A:C8
|
4.4
|
89.7
|
1.0
|
BR
|
A:BR102
|
4.4
|
83.9
|
0.5
|
N3
|
A:C8
|
4.4
|
72.8
|
1.0
|
C2'
|
A:C7
|
4.4
|
76.1
|
1.0
|
O5'
|
A:C8
|
4.6
|
79.7
|
1.0
|
O2
|
A:C7
|
4.6
|
73.8
|
1.0
|
O5'
|
A:C7
|
4.7
|
71.6
|
1.0
|
P
|
A:C8
|
4.8
|
0.1
|
1.0
|
C1'
|
A:C7
|
4.8
|
70.6
|
1.0
|
C2
|
A:C8
|
4.9
|
89.8
|
1.0
|
|
Bromine binding site 3 out
of 4 in 6qn3
Go back to
Bromine Binding Sites List in 6qn3
Bromine binding site 3 out
of 4 in the Structure of the Glutamine II Riboswitch
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Structure of the Glutamine II Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br203
b:71.1
occ:0.50
|
C5
|
B:C9
|
2.1
|
98.6
|
1.0
|
N4
|
B:C9
|
2.7
|
81.3
|
1.0
|
C4
|
B:C9
|
2.8
|
81.0
|
1.0
|
C6
|
B:C9
|
3.3
|
88.9
|
1.0
|
C5
|
B:C8
|
3.5
|
0.5
|
1.0
|
OP2
|
B:C9
|
3.6
|
78.8
|
1.0
|
C4
|
B:C8
|
3.6
|
0.7
|
1.0
|
C6
|
B:C8
|
3.8
|
91.2
|
1.0
|
O4
|
B:U10
|
3.9
|
0.6
|
1.0
|
N3
|
B:C8
|
3.9
|
73.6
|
1.0
|
BR
|
B:BR204
|
4.0
|
85.8
|
0.5
|
N4
|
B:C8
|
4.0
|
0.2
|
1.0
|
N3
|
B:C9
|
4.1
|
82.4
|
1.0
|
N1
|
B:C8
|
4.1
|
82.0
|
1.0
|
C2
|
B:C8
|
4.2
|
77.2
|
1.0
|
C5
|
B:U10
|
4.2
|
93.2
|
1.0
|
C4
|
B:U10
|
4.3
|
0.5
|
1.0
|
N1
|
B:C9
|
4.4
|
81.6
|
1.0
|
C3'
|
B:C8
|
4.7
|
72.7
|
1.0
|
C2'
|
B:C8
|
4.8
|
89.5
|
1.0
|
C2
|
B:C9
|
4.8
|
91.7
|
1.0
|
P
|
B:C9
|
4.8
|
99.8
|
1.0
|
O5'
|
B:C9
|
4.9
|
0.2
|
1.0
|
O2
|
B:C8
|
5.0
|
84.6
|
1.0
|
|
Bromine binding site 4 out
of 4 in 6qn3
Go back to
Bromine Binding Sites List in 6qn3
Bromine binding site 4 out
of 4 in the Structure of the Glutamine II Riboswitch
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 4 of Structure of the Glutamine II Riboswitch within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Br204
b:85.8
occ:0.50
|
C5
|
B:C8
|
1.9
|
0.5
|
1.0
|
C4
|
B:C8
|
2.8
|
0.7
|
1.0
|
N4
|
B:C8
|
2.8
|
0.2
|
1.0
|
C6
|
B:C8
|
3.0
|
91.2
|
1.0
|
C4
|
B:C7
|
3.5
|
81.0
|
1.0
|
C5
|
B:C7
|
3.6
|
69.9
|
1.0
|
N3
|
B:C7
|
3.8
|
87.0
|
1.0
|
C6
|
B:C7
|
3.8
|
82.7
|
1.0
|
N1
|
B:C7
|
4.0
|
81.2
|
1.0
|
BR
|
B:BR203
|
4.0
|
71.1
|
0.5
|
C2
|
B:C7
|
4.0
|
78.6
|
1.0
|
N3
|
B:C8
|
4.0
|
73.6
|
1.0
|
N4
|
B:C7
|
4.1
|
69.9
|
1.0
|
OP2
|
B:C8
|
4.1
|
79.0
|
1.0
|
N1
|
B:C8
|
4.2
|
82.0
|
1.0
|
C3'
|
B:C7
|
4.5
|
67.7
|
1.0
|
C2
|
B:C8
|
4.6
|
77.2
|
1.0
|
C2'
|
B:C7
|
4.7
|
74.3
|
1.0
|
O2
|
B:C7
|
4.7
|
65.1
|
1.0
|
O5'
|
B:C8
|
4.8
|
80.0
|
1.0
|
C1'
|
B:C7
|
4.9
|
65.4
|
1.0
|
|
Reference:
L.Huang,
J.Wang,
A.M.Watkins,
R.Das,
D.M.J.Lilley.
Structure and Ligand Binding of the Glutamine-II Riboswitch. Nucleic Acids Res. V. 47 7666 2019.
ISSN: ESSN 1362-4962
PubMed: 31216023
DOI: 10.1093/NAR/GKZ539
Page generated: Thu Jul 11 02:32:15 2024
|