Atomistry » Sodium » PDB 2qd8-2r22 » 2r22
Atomistry »
  Sodium »
    PDB 2qd8-2r22 »
      2r22 »

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

Go back to Sodium Binding Sites List in 2r22
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: Mon Oct 7 04:07:31 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy