Barium in PDB 5fkf: Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
Protein crystallography data
The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc, PDB code: 5fkf
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)
|
57.410 /
2.80
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.810,
61.810,
154.940,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.45 /
25.75
|
Other elements in 5fkf:
The structure of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc also contains other interesting chemical elements:
Barium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Barium atom in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
(pdb code 5fkf). This binding sites where shown within
5.0 Angstroms radius around Barium atom.
In total 12 binding sites of Barium where determined in the
Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc, PDB code: 5fkf:
Jump to Barium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Barium binding site 1 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 1 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_01.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 1 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1096
b:0.7
occ:0.99
|
O6
|
A:G86
|
2.9
|
93.4
|
1.0
|
N7
|
A:G86
|
3.1
|
65.7
|
1.0
|
C6
|
A:G86
|
3.6
|
69.8
|
1.0
|
C5
|
A:G86
|
3.6
|
59.1
|
1.0
|
N7
|
A:A85
|
4.1
|
73.9
|
1.0
|
C8
|
A:G86
|
4.2
|
49.1
|
1.0
|
N6
|
A:A87
|
4.5
|
51.5
|
1.0
|
OP2
|
A:A85
|
4.5
|
96.9
|
1.0
|
C5
|
A:A85
|
4.6
|
74.9
|
1.0
|
N6
|
A:A85
|
4.6
|
90.7
|
1.0
|
C8
|
A:A85
|
4.7
|
74.8
|
1.0
|
C6
|
A:A85
|
4.9
|
79.9
|
1.0
|
N1
|
A:G86
|
4.9
|
59.9
|
1.0
|
C4
|
A:G86
|
4.9
|
44.2
|
1.0
|
N7
|
A:A87
|
5.0
|
51.6
|
1.0
|
|
Barium binding site 2 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 2 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_02.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 2 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1097
b:0.8
occ:0.80
|
O6
|
A:G32
|
3.0
|
48.4
|
1.0
|
N7
|
A:G32
|
3.0
|
79.7
|
1.0
|
C6
|
A:G32
|
3.5
|
47.8
|
1.0
|
C5
|
A:G32
|
3.5
|
72.0
|
1.0
|
C8
|
A:G32
|
4.2
|
55.9
|
1.0
|
N4
|
A:C31
|
4.3
|
65.0
|
1.0
|
C5
|
A:C31
|
4.3
|
46.0
|
1.0
|
OP2
|
A:C31
|
4.4
|
59.4
|
1.0
|
C4
|
A:C31
|
4.5
|
45.9
|
1.0
|
C4
|
A:G32
|
4.8
|
46.8
|
1.0
|
N1
|
A:G32
|
4.8
|
47.9
|
1.0
|
|
Barium binding site 3 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 3 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_03.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 3 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1098
b:0.6
occ:1.00
|
OP2
|
A:G1
|
2.8
|
59.5
|
1.0
|
O5'
|
A:G1
|
3.3
|
55.8
|
1.0
|
P
|
A:G1
|
3.6
|
63.8
|
1.0
|
C5'
|
A:G1
|
4.2
|
55.3
|
1.0
|
C8
|
A:G1
|
4.4
|
59.2
|
1.0
|
OP1
|
A:G1
|
4.7
|
65.5
|
1.0
|
N7
|
A:G1
|
4.7
|
73.8
|
1.0
|
|
Barium binding site 4 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 4 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_04.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 4 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1099
b:54.9
occ:0.69
|
O2'
|
A:U64
|
2.8
|
65.4
|
1.0
|
O4
|
A:U67
|
2.9
|
97.6
|
1.0
|
O2
|
A:U64
|
3.3
|
92.2
|
1.0
|
C4
|
A:U67
|
3.9
|
72.5
|
1.0
|
C2'
|
A:U64
|
3.9
|
69.9
|
1.0
|
C1'
|
A:U64
|
4.1
|
72.2
|
1.0
|
C2
|
A:U64
|
4.1
|
71.9
|
1.0
|
OP2
|
A:C66
|
4.3
|
56.7
|
1.0
|
C5
|
A:U67
|
4.4
|
68.2
|
1.0
|
O3'
|
A:U64
|
4.5
|
77.7
|
1.0
|
N1
|
A:U64
|
4.5
|
59.5
|
1.0
|
N4
|
A:C25
|
4.6
|
76.1
|
1.0
|
O6
|
A:G68
|
4.7
|
51.9
|
1.0
|
C3'
|
A:U64
|
4.9
|
75.7
|
1.0
|
|
Barium binding site 5 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 5 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_05.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 5 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1100
b:0.0
occ:1.00
|
N7
|
A:G50
|
2.7
|
0.4
|
1.0
|
O6
|
A:G50
|
3.0
|
0.9
|
1.0
|
C5
|
A:G50
|
3.4
|
0.4
|
1.0
|
C6
|
A:G50
|
3.5
|
0.7
|
1.0
|
OP1
|
A:A52
|
3.8
|
0.6
|
1.0
|
C8
|
A:G50
|
3.8
|
0.4
|
1.0
|
C4
|
A:G50
|
4.6
|
0.1
|
1.0
|
N7
|
A:A49
|
4.8
|
68.5
|
1.0
|
N1
|
A:G50
|
4.8
|
0.8
|
1.0
|
N9
|
A:G50
|
4.9
|
0.7
|
1.0
|
|
Barium binding site 6 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 6 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_06.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 6 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1101
b:0.7
occ:1.00
|
O6
|
A:G74
|
2.3
|
68.9
|
1.0
|
N7
|
A:G74
|
2.7
|
0.7
|
1.0
|
C6
|
A:G74
|
2.7
|
0.8
|
1.0
|
C5
|
A:G74
|
2.9
|
1.0
|
1.0
|
C8
|
A:G74
|
3.8
|
0.6
|
1.0
|
N1
|
A:G74
|
4.0
|
0.2
|
1.0
|
C4
|
A:G74
|
4.1
|
71.5
|
1.0
|
N9
|
A:G74
|
4.6
|
68.3
|
1.0
|
OP1
|
A:A76
|
4.6
|
79.8
|
1.0
|
N7
|
A:G73
|
4.8
|
71.7
|
1.0
|
OP2
|
A:A76
|
4.9
|
78.0
|
1.0
|
C2
|
A:G74
|
4.9
|
86.3
|
1.0
|
OP2
|
A:G73
|
5.0
|
87.2
|
1.0
|
|
Barium binding site 7 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 7 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_07.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 7 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1102
b:0.4
occ:1.00
|
OP1
|
A:G1
|
3.2
|
65.5
|
1.0
|
OP2
|
A:G1
|
3.6
|
59.5
|
1.0
|
P
|
A:G1
|
3.9
|
63.8
|
1.0
|
N7
|
A:G1
|
4.7
|
73.8
|
1.0
|
O5'
|
A:G1
|
4.8
|
55.8
|
1.0
|
|
Barium binding site 8 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 8 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_08.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 8 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1103
b:0.1
occ:0.99
|
O6
|
A:G11
|
2.7
|
95.3
|
1.0
|
OP1
|
A:U64
|
3.3
|
79.7
|
1.0
|
C6
|
A:G11
|
3.7
|
80.5
|
1.0
|
N1
|
A:G11
|
4.1
|
68.2
|
1.0
|
N6
|
A:A12
|
4.2
|
79.0
|
1.0
|
OXT
|
A:SAM1095
|
4.2
|
68.4
|
1.0
|
O2'
|
A:C8
|
4.3
|
64.2
|
1.0
|
P
|
A:U64
|
4.3
|
74.4
|
1.0
|
OP2
|
A:U64
|
4.6
|
62.0
|
1.0
|
O5'
|
A:U64
|
4.7
|
73.8
|
1.0
|
|
Barium binding site 9 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 9 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_09.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 9 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1104
b:0.9
occ:1.00
|
N7
|
A:G55
|
3.6
|
0.9
|
1.0
|
N6
|
A:A45
|
3.6
|
72.0
|
1.0
|
N1
|
A:A45
|
3.7
|
71.0
|
1.0
|
N1
|
A:A46
|
3.8
|
65.9
|
1.0
|
C6
|
A:A45
|
4.1
|
70.8
|
1.0
|
C2
|
A:A46
|
4.2
|
64.1
|
1.0
|
C8
|
A:G55
|
4.2
|
97.2
|
1.0
|
C5
|
A:G55
|
4.4
|
96.2
|
1.0
|
OP2
|
A:G55
|
4.5
|
98.5
|
1.0
|
O6
|
A:G55
|
4.6
|
96.6
|
1.0
|
C6
|
A:G55
|
4.7
|
96.0
|
1.0
|
C2
|
A:A45
|
4.8
|
70.0
|
1.0
|
O6
|
A:G56
|
4.9
|
91.9
|
1.0
|
C6
|
A:A46
|
5.0
|
67.1
|
1.0
|
|
Barium binding site 10 out
of 12 in 5fkf
Go back to
Barium Binding Sites List in 5fkf
Barium binding site 10 out
of 12 in the Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_10.jpg) Mono view
![](/pictures/BA/pdb/fk/5fkf-BA-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 10 of Sam-I Riboswitch Bearing the H. Marismortui Kt-7 Variant 3BN Is Uc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba1113
b:0.7
occ:1.00
|
O6
|
A:G94
|
3.3
|
58.0
|
1.0
|
C6
|
A:G94
|
4.3
|
64.2
|
1.0
|
N1
|
A:G94
|
4.7
|
92.3
|
1.0
|
|
Reference:
L.Huang,
J.Wang,
D.M.J.Lilley.
A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function. Nucleic Acids Res. V. 44 5390 2016.
ISSN: ISSN 0305-1048
PubMed: 27016741
DOI: 10.1093/NAR/GKW201
Page generated: Wed Jul 10 15:46:55 2024
|