Sodium in PDB 2r21: Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)
Protein crystallography data
The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn), PDB code: 2r21
was solved by
Y.Timsit,
S.Bombard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.59
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
25.250,
25.650,
29.720,
98.13,
106.15,
100.83
|
R / Rfree (%)
|
16.9 /
19.1
|
Other elements in 2r21:
The structure of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn) also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)
(pdb code 2r21). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn), PDB code: 2r21:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 2r21
Go back to
Sodium Binding Sites List in 2r21
Sodium binding site 1 out
of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na14
b:15.2
occ:1.00
|
O
|
A:HOH89
|
2.3
|
24.6
|
0.8
|
O
|
A:HOH37
|
2.3
|
24.2
|
1.0
|
O
|
A:HOH49
|
2.5
|
21.5
|
0.9
|
O4
|
A:U4
|
2.5
|
9.6
|
1.0
|
O4
|
A:U5
|
2.5
|
10.3
|
1.0
|
O
|
A:HOH53
|
2.5
|
18.8
|
1.0
|
O
|
B:HOH73
|
2.8
|
28.3
|
1.0
|
C4
|
A:U4
|
3.3
|
8.7
|
1.0
|
C4
|
A:U5
|
3.5
|
8.5
|
1.0
|
C5
|
A:U4
|
3.7
|
7.1
|
1.0
|
C5
|
A:U5
|
4.1
|
9.5
|
1.0
|
N6
|
B:A22
|
4.1
|
9.9
|
1.0
|
O
|
A:HOH20
|
4.4
|
15.6
|
1.0
|
O
|
A:HOH26
|
4.4
|
12.2
|
1.0
|
N3
|
A:U4
|
4.4
|
8.2
|
1.0
|
O
|
A:HOH55
|
4.4
|
24.7
|
1.0
|
O
|
A:HOH25
|
4.4
|
14.5
|
1.0
|
N6
|
B:A23
|
4.6
|
9.9
|
1.0
|
N3
|
A:U5
|
4.6
|
9.3
|
1.0
|
O
|
A:HOH21
|
4.9
|
18.9
|
1.0
|
C6
|
A:U4
|
4.9
|
8.3
|
1.0
|
|
Sodium binding site 2 out
of 4 in 2r21
Go back to
Sodium Binding Sites List in 2r21
Sodium binding site 2 out
of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na15
b:18.2
occ:1.00
|
O
|
A:HOH31
|
2.5
|
15.4
|
1.0
|
O
|
A:HOH51
|
2.5
|
20.3
|
1.0
|
O
|
A:HOH71
|
2.5
|
28.1
|
0.9
|
N7
|
A:G7
|
2.6
|
11.8
|
1.0
|
O
|
A:HOH68
|
2.6
|
19.2
|
0.9
|
O
|
A:HOH58
|
2.6
|
20.5
|
1.0
|
C8
|
A:G7
|
3.3
|
10.2
|
1.0
|
C5
|
A:G7
|
3.6
|
8.9
|
1.0
|
O6
|
A:G7
|
4.1
|
11.4
|
1.0
|
C6
|
A:G7
|
4.2
|
10.4
|
1.0
|
OP2
|
A:G7
|
4.2
|
10.4
|
1.0
|
BR
|
A:5BU6
|
4.4
|
17.3
|
1.0
|
C5
|
A:5BU6
|
4.4
|
11.6
|
1.0
|
N9
|
A:G7
|
4.4
|
9.8
|
1.0
|
C4
|
A:G7
|
4.6
|
9.0
|
1.0
|
C4
|
A:5BU6
|
4.7
|
11.3
|
1.0
|
C6
|
A:5BU6
|
4.7
|
10.6
|
1.0
|
OP2
|
A:A8
|
4.8
|
14.1
|
1.0
|
O5'
|
A:G7
|
4.9
|
10.0
|
1.0
|
|
Sodium binding site 3 out
of 4 in 2r21
Go back to
Sodium Binding Sites List in 2r21
Sodium binding site 3 out
of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na16
b:38.5
occ:0.67
|
O
|
A:HOH92
|
2.3
|
34.7
|
1.0
|
O
|
A:HOH52
|
2.5
|
23.1
|
0.9
|
O
|
A:HOH93
|
2.5
|
36.7
|
0.9
|
N7
|
A:A9
|
2.7
|
7.3
|
1.0
|
O
|
A:HOH67
|
2.9
|
19.1
|
1.0
|
C8
|
A:A9
|
3.6
|
8.5
|
1.0
|
C5
|
A:A9
|
3.8
|
8.4
|
1.0
|
N6
|
A:A9
|
3.9
|
9.0
|
1.0
|
OP2
|
A:A9
|
3.9
|
9.8
|
1.0
|
O
|
A:HOH75
|
4.1
|
23.0
|
1.0
|
C6
|
A:A9
|
4.3
|
7.8
|
1.0
|
O
|
B:HOH65
|
4.5
|
20.9
|
1.0
|
N7
|
A:A8
|
4.5
|
10.4
|
1.0
|
O
|
B:HOH89
|
4.6
|
28.9
|
0.8
|
O
|
A:HOH90
|
4.8
|
32.4
|
1.0
|
O
|
A:HOH58
|
4.8
|
20.5
|
1.0
|
N9
|
A:A9
|
4.8
|
7.9
|
1.0
|
C8
|
A:A8
|
4.9
|
8.9
|
1.0
|
C4
|
A:A9
|
4.9
|
9.1
|
1.0
|
C5
|
A:A8
|
5.0
|
8.7
|
1.0
|
|
Sodium binding site 4 out
of 4 in 2r21
Go back to
Sodium Binding Sites List in 2r21
Sodium binding site 4 out
of 4 in the Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn)
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of the Rna Brominated Tridecamer R(Gcguu- 5BUGAAACGC) at 1.6 A (Brmn) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1
b:22.4
occ:0.96
|
O
|
B:HOH65
|
2.3
|
20.9
|
1.0
|
O4
|
B:U18
|
2.4
|
11.2
|
1.0
|
O
|
B:HOH66
|
2.4
|
26.6
|
1.0
|
O4
|
B:U17
|
2.4
|
12.4
|
1.0
|
O
|
B:HOH44
|
2.5
|
22.0
|
1.0
|
O
|
B:HOH67
|
2.5
|
20.0
|
1.0
|
C4
|
B:U17
|
3.3
|
12.0
|
1.0
|
C4
|
B:U18
|
3.3
|
8.6
|
1.0
|
C5
|
B:U17
|
3.7
|
10.6
|
1.0
|
C5
|
B:U18
|
3.8
|
9.1
|
1.0
|
O
|
B:HOH108
|
3.8
|
35.1
|
1.0
|
N6
|
A:A9
|
4.0
|
9.0
|
1.0
|
O
|
B:HOH48
|
4.1
|
18.3
|
1.0
|
O
|
B:HOH36
|
4.3
|
19.3
|
1.0
|
O
|
B:HOH38
|
4.3
|
21.6
|
1.0
|
N3
|
B:U17
|
4.4
|
10.7
|
1.0
|
N3
|
B:U18
|
4.4
|
7.5
|
1.0
|
N6
|
A:A10
|
4.4
|
10.9
|
1.0
|
O
|
B:HOH49
|
4.4
|
23.3
|
1.0
|
O
|
A:HOH92
|
4.6
|
34.7
|
1.0
|
O
|
B:HOH37
|
5.0
|
16.4
|
1.0
|
C6
|
B:U17
|
5.0
|
10.5
|
1.0
|
|
Reference:
Y.Timsit,
S.Bombard.
1.3 A Resolution Structure of the Tridecamer R(Gcguuugaaacgc) To Be Published.
Page generated: Mon Oct 7 04:07:03 2024
|