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Potassium in PDB 3nd3: Uhelix 16-Mer Dsrna

Protein crystallography data

The structure of Uhelix 16-Mer Dsrna, PDB code: 3nd3 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) 18.31 / 1.37
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 42.735, 42.735, 126.358, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 22.9

Other elements in 3nd3:

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

Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Uhelix 16-Mer Dsrna (pdb code 3nd3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Uhelix 16-Mer Dsrna, PDB code: 3nd3:

Potassium binding site 1 out of 1 in 3nd3

Go back to Potassium Binding Sites List in 3nd3
Potassium binding site 1 out of 1 in the Uhelix 16-Mer Dsrna


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Uhelix 16-Mer Dsrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K17

b:28.4
occ:0.18
H5' A:U14 2.9 27.0 1.0
O2' A:U13 3.0 23.9 1.0
HO2' A:U13 3.2 28.7 1.0
H4' A:U13 3.5 24.4 1.0
O3' A:U13 3.5 22.0 1.0
C5' A:U14 3.9 22.5 1.0
C2' A:U13 4.1 21.8 1.0
C3' A:U13 4.2 20.6 1.0
C4' A:U13 4.3 20.3 1.0
H5'' A:U14 4.3 27.0 1.0
OP1 A:U14 4.5 23.0 1.0
O5' A:U14 4.5 21.4 1.0
P A:U14 4.5 21.1 1.0
H4' A:U14 4.6 26.0 1.0
H2' A:U13 4.7 26.1 1.0
C4' A:U14 4.7 21.7 1.0
O A:HOH72 4.7 46.1 1.0
O A:HOH20 4.8 25.3 1.0
O4' A:U14 4.8 20.4 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: Sun Dec 13 23:20:38 2020

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