Atomistry » Sodium » PDB 3n0u-3nrv » 3nd4
Atomistry »
  Sodium »
    PDB 3n0u-3nrv »
      3nd4 »

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: Mon Oct 7 11:50:05 2024

Last articles

Mo in 9CU2
Mo in 9CU1
Mo in 8RHP
Mo in 9CU0
Mo in 9CTZ
Mo in 9CJD
Mo in 9CJF
Mo in 9CJC
Mo in 9CJE
Mo in 9CJB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy