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Sodium in PDB 2r22: Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn)

Protein crystallography data

The structure of Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn), PDB code: 2r22 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 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 25.280, 25.500, 29.600, 97.97, 106.69, 101.62
R / Rfree (%) 17.8 / 20

Other elements in 2r22:

The structure of Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn) also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn) (pdb code 2r22). 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 Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn), PDB code: 2r22:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2r22

Go back to Sodium Binding Sites List in 2r22
Sodium binding site 1 out of 4 in the Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn)


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 Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na14

b:31.4
occ:0.78
O A:HOH37 2.2 30.5 1.0
O A:HOH51 2.4 28.1 1.0
O A:HOH48 2.4 29.1 0.8
O4 A:U4 2.6 10.5 1.0
O4 A:U5 2.7 12.7 1.0
O B:HOH69 2.9 31.8 0.8
C4 A:U4 3.4 10.1 1.0
C5 A:U4 3.7 9.7 1.0
C4 A:U5 3.7 9.7 1.0
O A:HOH53 4.2 32.5 1.0
N6 B:A22 4.2 11.6 1.0
O A:HOH26 4.2 13.7 1.0
C5 A:U5 4.3 9.1 1.0
O B:HOH70 4.5 35.1 1.0
O A:HOH20 4.5 20.5 1.0
N3 A:U4 4.5 9.5 1.0
O A:HOH25 4.6 19.7 1.0
N6 B:A23 4.8 10.9 1.0
N3 A:U5 4.8 10.0 1.0
C6 A:U4 4.9 10.2 1.0

Sodium binding site 2 out of 4 in 2r22

Go back to Sodium Binding Sites List in 2r22
Sodium binding site 2 out of 4 in the Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn)


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 Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na15

b:17.2
occ:0.99
O A:HOH83 2.4 18.3 1.0
O A:HOH31 2.4 20.7 1.0
O A:HOH65 2.5 22.9 1.0
N7 A:G7 2.5 10.2 1.0
O A:HOH67 2.6 27.7 0.9
O A:HOH55 2.6 23.7 1.0
C8 A:G7 3.2 9.5 1.0
C5 A:G7 3.5 9.4 1.0
O6 A:G7 4.0 10.2 1.0
C6 A:G7 4.1 10.1 1.0
O A:HOH84 4.2 17.2 1.0
OP2 A:G7 4.2 11.7 1.0
N9 A:G7 4.4 8.7 1.0
C4 A:G7 4.5 8.0 1.0
C5 A:U6 4.6 10.6 1.0
OP2 A:A8 4.6 15.1 1.0
O5' A:G7 4.8 9.9 1.0
C4 A:U6 4.9 9.8 1.0
C6 A:U6 4.9 10.1 1.0
OP2 A:U6 5.0 13.1 1.0
N7 A:A8 5.0 9.8 1.0

Sodium binding site 3 out of 4 in 2r22

Go back to Sodium Binding Sites List in 2r22
Sodium binding site 3 out of 4 in the Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn)


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 Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na16

b:28.4
occ:0.87
O A:HOH73 2.3 28.5 1.0
O A:HOH50 2.4 22.1 1.0
O A:HOH75 2.5 43.4 1.0
O A:HOH64 2.7 19.9 1.0
N7 A:A9 2.8 10.3 1.0
C8 A:A9 3.6 10.4 1.0
C5 A:A9 3.7 10.9 1.0
N6 A:A9 3.8 11.5 1.0
O A:HOH71 3.9 16.4 1.0
OP2 A:A9 4.1 13.2 1.0
C6 A:A9 4.2 11.0 1.0
N7 A:A8 4.7 9.8 1.0
N9 A:A9 4.8 10.3 1.0
C4 A:A9 4.9 10.7 1.0
O A:HOH55 4.9 23.7 1.0

Sodium binding site 4 out of 4 in 2r22

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Sodium binding site 4 out of 4 in the Structure of the Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn)


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 Native Rna Tridecamer R(Gcguuugaaacgc) at 1.5 A (Natmn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1

b:28.7
occ:0.81
O4 B:U18 2.4 11.3 1.0
O B:HOH61 2.4 25.2 0.9
O B:HOH62 2.5 23.4 1.0
O B:HOH42 2.5 29.8 0.9
O4 B:U17 2.5 12.3 1.0
C4 B:U18 3.3 9.4 1.0
C4 B:U17 3.4 10.5 1.0
C5 B:U17 3.8 10.0 1.0
N6 A:A9 3.9 11.5 1.0
C5 B:U18 3.9 9.9 1.0
O B:HOH47 4.1 30.4 1.0
O B:HOH46 4.1 18.8 1.0
O B:HOH37 4.2 17.5 1.0
O B:HOH35 4.3 24.2 1.0
N3 B:U18 4.4 9.7 1.0
O B:HOH71 4.4 28.5 1.0
N6 A:A10 4.5 9.8 1.0
N3 B:U17 4.5 10.0 1.0
O B:HOH36 5.0 18.1 1.0

Reference:

Y.Timsit, S.Bombard. The 1.3 A Structure of the Tridecamer R(Gcguuugaaacgc) To Be Published.
Page generated: Tue Dec 15 05:55:40 2020

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