Sodium in PDB 6s7d: Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate

The structure of Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate, PDB code: 6s7d was solved by P.F.Conlon, J.Steinhogl, J.S.Vyle, J.P.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.57 / 1.45
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	38.642, 38.642, 79.307, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 23.7

The structure of Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate also contains other interesting chemical elements:

Barium	(Ba)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate (pdb code 6s7d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate, PDB code: 6s7d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:33.0 occ:1.00 O A:HOH210 2.4 30.0 0.1 N7 A:DG6 2.7 20.6 1.0 O A:HOH206 3.0 19.3 1.0 O A:HOH210 3.1 31.7 0.9 H5 A:DC5 3.5 25.7 1.0 C8 A:DG6 3.5 20.8 1.0 H8 A:DG6 3.6 24.9 1.0 O A:HOH219 3.6 34.0 1.0 C5 A:DC5 3.6 21.4 1.0 C5 A:DG6 3.8 20.9 1.0 C4 A:DC5 3.9 21.2 1.0 O6 A:DG6 3.9 19.7 1.0 C6 A:DC5 4.0 21.8 1.0 H41 A:DC5 4.2 25.0 1.0 H6 A:DC5 4.2 26.1 1.0 N4 A:DC5 4.2 20.9 1.0 C6 A:DG6 4.2 20.6 1.0 H3' A:DC5 4.2 28.4 1.0 OP2 A:DG6 4.3 23.3 1.0 O A:HOH211 4.4 24.2 1.0 N7 A:DG7 4.5 20.7 1.0 N3 A:DC5 4.6 22.0 1.0 N1 A:DC5 4.7 22.2 1.0 H42 A:DC5 4.7 25.0 1.0 CL A:CL103 4.8 22.1 1.0 N9 A:DG6 4.8 21.7 1.0 H2' A:DC5 4.8 27.9 1.0 OP2 A:DC5 4.9 27.7 1.0 C4 A:DG6 4.9 21.4 1.0 C2 A:DC5 4.9 21.9 1.0

Sodium binding site 2 out of 2 in the Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:37.5 occ:1.00 N7 B:DA9 2.5 24.8 1.0 O B:HOH222 2.6 30.6 1.0 H62 B:DA9 2.7 31.0 1.0 O B:HOH216 2.9 28.6 1.0 O B:HOH208 3.3 19.8 1.0 C8 B:DA9 3.5 24.7 1.0 N6 B:DA9 3.5 25.9 1.0 C5 B:DA9 3.5 25.2 1.0 H8 B:DA9 3.6 29.6 1.0 H3' B:DG8 3.7 27.8 1.0 OP2 B:DA9 3.8 23.4 1.0 N7 B:DG8 3.8 21.2 1.0 H41 B:DC10 3.9 27.7 1.0 C8 B:DG8 3.9 21.6 1.0 C6 B:DA9 3.9 25.3 1.0 O B:HOH219 3.9 30.7 1.0 H8 B:DG8 4.0 25.8 1.0 H2' B:DG8 4.1 27.5 1.0 H61 B:DA9 4.2 31.0 1.0 C5 B:DG8 4.2 21.8 1.0 N9 B:DG8 4.3 21.9 1.0 N4 B:DC10 4.4 23.1 1.0 C4 B:DG8 4.5 21.8 1.0 C3' B:DG8 4.5 23.2 1.0 N9 B:DA9 4.7 24.2 1.0 C4 B:DA9 4.7 24.6 1.0 H42 B:DC10 4.7 27.7 1.0 C2' B:DG8 4.7 22.9 1.0 H5 B:DC10 4.8 27.6 1.0 O B:HOH217 4.8 30.8 1.0 C6 B:DG8 4.9 21.6 1.0 P B:DA9 4.9 23.6 1.0 O5' B:DA9 5.0 23.1 1.0

P.F.Conlon, O.Eguaogie, J.J.Wilson, J.S.T.Sweet, J.Steinhoegl, O.Hancox, K.Englert, C.J.Law, S.A.Allman, J.H.R.Tucker, J.P.Hall, J.S.Vyle. Solid-Phase Synthesis and Structural Characterisation of Phosphoroselenolate-Modified Dna: A Backbone Analogue Which Does Not Impose Conformational Bias and Facilitates Sad X-Ray Crystallography Chem Sci 2019.
ISSN: ESSN 2041-6539
DOI: 10.1039/C9SC04098F