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Sodium in PDB 3nd4: Watson-Crick 16-Mer Dsrna

Protein crystallography data

The structure of Watson-Crick 16-Mer Dsrna, PDB code: 3nd4 was solved by B.H.Mooers, A.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.39 / 1.52
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 41.094, 41.094, 123.690, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 21.4

Other elements in 3nd4:

The structure of Watson-Crick 16-Mer Dsrna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Watson-Crick 16-Mer Dsrna (pdb code 3nd4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Watson-Crick 16-Mer Dsrna, PDB code: 3nd4:

Sodium binding site 1 out of 1 in 3nd4

Go back to Sodium Binding Sites List in 3nd4
Sodium binding site 1 out of 1 in the Watson-Crick 16-Mer Dsrna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Watson-Crick 16-Mer Dsrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na19

b:17.9
occ:1.00
O A:HOH219 2.2 28.0 1.0
O A:HOH519 2.2 25.2 1.0
O A:HOH319 2.4 22.2 1.0
O A:HOH119 2.6 21.9 1.0
O A:HOH419 2.6 22.1 1.0
N7 A:A3 2.6 9.7 1.0
H62 A:A3 2.8 10.2 1.0
C8 A:A3 3.6 8.8 1.0
C5 A:A3 3.6 9.4 1.0
N6 A:A3 3.7 8.5 1.0
H8 A:A3 3.7 10.6 1.0
C6 A:A3 4.0 7.3 1.0
O A:HOH91 4.1 24.5 1.0
N7 A:G2 4.2 10.6 1.0
OP2 A:A3 4.3 15.2 1.0
H61 A:A3 4.5 10.2 1.0
C8 A:G2 4.6 10.2 1.0
H3' A:G2 4.7 15.8 1.0
N9 A:A3 4.8 10.1 1.0
C5 A:G2 4.8 9.7 1.0
OP2 A:G2 4.8 12.7 1.0
C4 A:A3 4.8 9.8 1.0
H8 A:G2 4.8 12.2 1.0
O6 A:G4 4.8 10.3 1.0

Reference:

B.H.Mooers, A.Singh. The Crystal Structure of An Oligo(U):Pre-Mrna Duplex From A Trypanosome Rna Editing Substrate. Rna V. 17 1870 2011.
ISSN: ISSN 1355-8382
PubMed: 21878548
DOI: 10.1261/RNA.2880311
Page generated: Tue Dec 15 06:18:58 2020

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