Barium in PDB 3iqr: Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Protein crystallography data
The structure of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam, PDB code: 3iqr
was solved by
R.K.Montange,
R.T.Batey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.93 /
2.55
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.804,
61.804,
157.568,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.9 /
29.3
|
Barium Binding Sites:
The binding sites of Barium atom in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
(pdb code 3iqr). This binding sites where shown within
5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the
Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam, PDB code: 3iqr:
Jump to Barium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Barium binding site 1 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 1 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 1 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba201
b:95.9
occ:1.00
|
N7
|
A:G50
|
2.9
|
61.3
|
1.0
|
O6
|
A:G50
|
3.1
|
62.0
|
1.0
|
O
|
A:HOH440
|
3.5
|
37.5
|
1.0
|
C5
|
A:G50
|
3.5
|
60.9
|
1.0
|
C6
|
A:G50
|
3.6
|
61.5
|
1.0
|
C8
|
A:G50
|
4.0
|
62.1
|
1.0
|
OP1
|
A:A52
|
4.1
|
86.1
|
1.0
|
OP2
|
A:A52
|
4.2
|
85.8
|
1.0
|
N7
|
A:A49
|
4.6
|
51.1
|
1.0
|
P
|
A:A52
|
4.6
|
86.4
|
1.0
|
C4
|
A:G50
|
4.8
|
61.2
|
1.0
|
N1
|
A:G50
|
4.9
|
61.6
|
1.0
|
N9
|
A:G50
|
5.0
|
62.7
|
1.0
|
|
Barium binding site 2 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 2 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 2 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba202
b:0.4
occ:1.00
|
O6
|
A:G18
|
2.7
|
65.9
|
1.0
|
C6
|
A:G18
|
3.8
|
62.4
|
1.0
|
C5
|
A:G18
|
4.5
|
62.3
|
1.0
|
N7
|
A:G18
|
4.5
|
61.8
|
1.0
|
OP2
|
A:U17
|
4.7
|
81.4
|
1.0
|
O4
|
A:U17
|
4.8
|
72.3
|
1.0
|
N1
|
A:G18
|
4.8
|
60.6
|
1.0
|
O6
|
A:G19
|
4.8
|
60.5
|
1.0
|
C5
|
A:U17
|
4.9
|
74.0
|
1.0
|
OP2
|
A:G16
|
5.0
|
77.8
|
1.0
|
|
Barium binding site 3 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 3 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 3 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba203
b:83.9
occ:1.00
|
O6
|
A:G74
|
2.7
|
50.4
|
1.0
|
N7
|
A:G74
|
3.1
|
50.0
|
1.0
|
C6
|
A:G74
|
3.4
|
47.9
|
1.0
|
C5
|
A:G74
|
3.5
|
47.9
|
1.0
|
O
|
A:HOH405
|
4.2
|
29.2
|
1.0
|
C8
|
A:G74
|
4.3
|
50.2
|
1.0
|
OP1
|
A:A76
|
4.3
|
50.7
|
1.0
|
N1
|
A:G74
|
4.6
|
46.4
|
1.0
|
C4
|
A:G74
|
4.8
|
48.0
|
1.0
|
OP2
|
A:A76
|
4.8
|
50.5
|
1.0
|
N7
|
A:G73
|
4.9
|
59.9
|
1.0
|
|
Barium binding site 4 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 4 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 4 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba204
b:57.7
occ:1.00
|
O2'
|
A:U64
|
2.9
|
59.9
|
1.0
|
O4
|
A:U67
|
3.0
|
43.5
|
1.0
|
O2
|
A:U64
|
3.1
|
51.3
|
1.0
|
C2'
|
A:U64
|
3.7
|
54.8
|
1.0
|
C4
|
A:U67
|
4.0
|
40.0
|
1.0
|
C2
|
A:U64
|
4.1
|
52.0
|
1.0
|
C5
|
A:U67
|
4.3
|
39.4
|
1.0
|
C1'
|
A:U64
|
4.3
|
54.4
|
1.0
|
OP2
|
A:C66
|
4.3
|
43.9
|
1.0
|
N4
|
A:C25
|
4.6
|
41.6
|
1.0
|
O6
|
A:G68
|
4.7
|
55.7
|
1.0
|
N1
|
A:U64
|
4.7
|
53.2
|
1.0
|
O
|
A:HOH419
|
4.7
|
30.5
|
1.0
|
|
Barium binding site 5 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 5 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 5 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba205
b:0.8
occ:1.00
|
N7
|
A:G32
|
3.9
|
60.1
|
1.0
|
C8
|
A:G32
|
4.6
|
59.5
|
1.0
|
OP2
|
A:G32
|
4.6
|
48.9
|
1.0
|
C5
|
A:G32
|
4.7
|
59.3
|
1.0
|
O6
|
A:G32
|
4.7
|
59.4
|
1.0
|
OP2
|
A:C31
|
4.7
|
51.6
|
1.0
|
|
Barium binding site 6 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 6 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 6 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba206
b:0.3
occ:1.00
|
OP2
|
A:A10
|
2.9
|
59.8
|
1.0
|
OP2
|
A:U64
|
3.2
|
46.0
|
1.0
|
O3'
|
A:U63
|
3.4
|
47.6
|
1.0
|
O3'
|
A:A9
|
3.6
|
64.4
|
1.0
|
P
|
A:A10
|
3.8
|
60.2
|
1.0
|
P
|
A:U64
|
3.8
|
45.2
|
1.0
|
OP1
|
A:A62
|
3.9
|
42.9
|
1.0
|
N7
|
A:G11
|
4.0
|
46.7
|
1.0
|
C4'
|
A:U63
|
4.1
|
46.6
|
1.0
|
O5'
|
A:A10
|
4.2
|
58.6
|
1.0
|
C3'
|
A:U63
|
4.3
|
47.2
|
1.0
|
O6
|
A:G11
|
4.3
|
47.5
|
1.0
|
OP1
|
A:U64
|
4.4
|
46.4
|
1.0
|
N7
|
A:A10
|
4.6
|
48.9
|
1.0
|
C5'
|
A:U63
|
4.7
|
47.2
|
1.0
|
OP2
|
A:G11
|
4.7
|
49.1
|
1.0
|
C8
|
A:A10
|
4.8
|
48.4
|
1.0
|
C5
|
A:G11
|
4.9
|
47.8
|
1.0
|
C3'
|
A:A9
|
4.9
|
66.9
|
1.0
|
C6
|
A:G11
|
5.0
|
48.0
|
1.0
|
C8
|
A:G11
|
5.0
|
45.8
|
1.0
|
|
Barium binding site 7 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 7 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 7 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba207
b:0.9
occ:1.00
|
N7
|
A:G86
|
3.1
|
51.7
|
1.0
|
O6
|
A:G86
|
3.3
|
50.5
|
1.0
|
C5
|
A:G86
|
3.8
|
50.1
|
1.0
|
C6
|
A:G86
|
3.9
|
50.9
|
1.0
|
N7
|
A:A85
|
4.0
|
56.9
|
1.0
|
C8
|
A:G86
|
4.2
|
50.7
|
1.0
|
N6
|
A:A85
|
4.4
|
57.7
|
1.0
|
C5
|
A:A85
|
4.5
|
58.1
|
1.0
|
C8
|
A:A85
|
4.7
|
56.7
|
1.0
|
C6
|
A:A85
|
4.7
|
57.8
|
1.0
|
N6
|
A:A87
|
4.7
|
46.2
|
1.0
|
OP2
|
A:A85
|
4.9
|
59.8
|
1.0
|
|
Barium binding site 8 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 8 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 8 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba208
b:0.2
occ:1.00
|
N1
|
A:A46
|
3.1
|
48.0
|
1.0
|
N7
|
A:G55
|
3.3
|
59.8
|
1.0
|
C2
|
A:A46
|
3.4
|
47.7
|
1.0
|
O6
|
A:G55
|
3.8
|
60.9
|
1.0
|
C5
|
A:G55
|
4.0
|
60.3
|
1.0
|
C6
|
A:G55
|
4.2
|
60.1
|
1.0
|
C8
|
A:G55
|
4.2
|
60.7
|
1.0
|
N1
|
A:A45
|
4.3
|
46.3
|
1.0
|
C6
|
A:A46
|
4.4
|
46.5
|
1.0
|
N6
|
A:A45
|
4.6
|
42.6
|
1.0
|
N3
|
A:A46
|
4.6
|
47.7
|
1.0
|
N6
|
A:A46
|
4.8
|
48.1
|
1.0
|
OP2
|
A:G55
|
4.8
|
75.1
|
1.0
|
C6
|
A:A45
|
4.9
|
46.1
|
1.0
|
O6
|
A:G56
|
5.0
|
51.5
|
1.0
|
|
Barium binding site 9 out
of 9 in 3iqr
Go back to
Barium Binding Sites List in 3iqr
Barium binding site 9 out
of 9 in the Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 9 of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound with Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba209
b:0.5
occ:1.00
|
N7
|
A:G1
|
2.9
|
53.7
|
1.0
|
O6
|
A:G1
|
3.5
|
57.9
|
1.0
|
C5
|
A:G1
|
3.8
|
54.5
|
1.0
|
C8
|
A:G1
|
4.0
|
54.7
|
1.0
|
C6
|
A:G1
|
4.0
|
55.2
|
1.0
|
O
|
A:HOH403
|
4.2
|
24.2
|
1.0
|
OP3
|
A:G1
|
4.5
|
64.2
|
1.0
|
O
|
A:HOH402
|
4.9
|
23.4
|
1.0
|
O6
|
A:G2
|
5.0
|
45.3
|
1.0
|
|
Reference:
C.D.Stoddard,
R.K.Montange,
S.P.Hennelly,
R.P.Rambo,
K.Y.Sanbonmatsu,
R.T.Batey.
Free State Conformational Sampling of the Sam-I Riboswitch Aptamer Domain. Structure V. 18 787 2010.
ISSN: ISSN 0969-2126
PubMed: 20637415
DOI: 10.1016/J.STR.2010.04.006
Page generated: Wed Jul 10 15:14:14 2024
|