Barium 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Barium 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 Barium atom.
In total 2 binding sites of Barium where determined in the Self-Complementary Duplex Dna Containing An Internucleoside Phosphoroselenolate, PDB code: 6s7d:
Jump to Barium binding site number: 1; 2;

Barium 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 Barium with other atoms in the Ba 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:Ba101 b:22.1 occ:1.00 O A:HOH211 2.7 24.2 1.0 O A:HOH210 2.8 31.7 0.9 O6 A:DG8 2.9 21.8 1.0 O A:HOH210 2.9 30.0 0.1 O6 A:DG7 3.1 20.1 1.0 N7 A:DG8 3.2 21.9 1.0 C6 A:DG8 3.6 22.1 1.0 O A:HOH222 3.7 37.7 1.0 C5 A:DG8 3.7 21.6 1.0 O A:HOH220 3.7 38.2 1.0 H42 B:DC3 3.8 27.8 1.0 O A:HOH219 3.9 34.0 1.0 C6 A:DG7 3.9 20.7 1.0 H42 B:DC4 4.2 28.3 1.0 N7 A:DG7 4.2 20.7 1.0 O A:HOH206 4.3 19.3 1.0 CL A:CL103 4.3 22.1 1.0 C5 A:DG7 4.4 20.8 1.0 C8 A:DG8 4.4 21.6 1.0 H61 A:DA9 4.5 27.6 1.0 N4 B:DC3 4.6 23.2 1.0 H41 B:DC3 4.7 27.8 1.0 H8 A:DG8 4.7 25.9 1.0 N4 B:DC4 4.8 23.6 1.0 N6 A:DA9 4.9 23.0 1.0 H62 A:DA9 4.9 27.6 1.0 N1 A:DG8 4.9 22.2 1.0 H41 B:DC4 4.9 28.3 1.0

Barium 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 Barium with other atoms in the Ba 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:Ba102 b:21.0 occ:1.00 O6 B:DG8 2.7 20.7 1.0 O B:HOH215 2.7 34.9 1.0 O B:HOH208 2.8 19.8 1.0 O A:HOH203 2.9 33.0 1.0 O B:HOH217 3.0 30.8 1.0 O B:HOH203 3.0 20.6 1.0 O6 B:DG7 3.0 23.8 1.0 N7 B:DG8 3.0 21.2 1.0 C6 B:DG8 3.4 21.6 1.0 C5 B:DG8 3.5 21.8 1.0 C6 B:DG7 3.6 23.5 1.0 H41 A:DC3 4.0 31.6 1.0 C5 B:DG7 4.0 23.7 1.0 H41 A:DC4 4.0 32.3 1.0 N7 B:DG7 4.0 23.8 1.0 O B:HOH230 4.3 10.8 0.7 C8 B:DG8 4.3 21.6 1.0 O B:HOH230 4.3 11.8 0.3 H62 B:DA9 4.4 31.0 1.0 H61 B:DA9 4.4 31.0 1.0 N1 B:DG7 4.5 23.5 1.0 N6 B:DA9 4.6 25.9 1.0 H8 B:DG8 4.6 25.8 1.0 N4 A:DC4 4.6 26.9 1.0 H1 B:DG7 4.7 28.1 1.0 N4 A:DC3 4.7 26.3 1.0 O B:HOH204 4.7 24.4 1.0 N1 B:DG8 4.8 22.2 1.0 H42 A:DC4 4.8 32.3 1.0 O B:HOH205 4.9 29.6 1.0 H42 A:DC3 4.9 31.6 1.0 O B:HOH232 4.9 30.8 1.0 C4 B:DG8 4.9 21.8 1.0 O B:HOH216 5.0 28.6 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