Sodium in PDB 284d: The Bi-Loop, A New General Four-Stranded Dna Motif

The structure of The Bi-Loop, A New General Four-Stranded Dna Motif, PDB code: 284d was solved by S.A.Salisbury, S.E.Wilson, H.R.Powell, O.Kennard, P.Lubini, G.M.Sheldrick, N.Escaja, E.Alazzouzi, A.Grandas, E.Pedroso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	22.844, 27.676, 55.370, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / n/a

The structure of The Bi-Loop, A New General Four-Stranded Dna Motif also contains other interesting chemical elements:

Barium

(Ba)

11 atoms

The binding sites of Sodium atom in the The Bi-Loop, A New General Four-Stranded Dna Motif (pdb code 284d). 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 The Bi-Loop, A New General Four-Stranded Dna Motif, PDB code: 284d:

Sodium binding site 1 out of 1 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Na19 b:7.6 occ:1.00 O2 A:DT2 2.8 8.6 1.0 O2 B:DT12 2.8 7.4 1.0 O2 A:DT6 2.8 8.0 1.0 O B:HOH32 2.8 8.2 1.0 O A:HOH31 2.8 7.6 1.0 O2 B:DT16 2.8 7.4 1.0 H2 B:DA11 3.0 16.7 1.0 H2 A:DA1 3.0 11.5 1.0 H2 B:DA15 3.1 10.7 1.0 H2 A:DA5 3.1 9.1 1.0 C2 B:DA11 3.8 11.2 1.0 C2 A:DT2 3.8 9.3 1.0 H1' B:DT12 3.9 11.3 1.0 C2 B:DA15 3.9 7.2 1.0 C2 A:DA5 3.9 6.1 1.0 C2 A:DT6 3.9 7.5 1.0 C2 A:DA1 3.9 7.7 1.0 C2 B:DT16 3.9 6.9 1.0 C2 B:DT12 3.9 7.7 1.0 H1' B:DT16 3.9 12.2 1.0 H1' A:DT6 3.9 11.3 1.0 H1' A:DT2 4.0 13.5 1.0 H73 A:DT7 4.1 18.6 1.0 H73 B:DT13 4.2 15.1 1.0 H3 A:DT2 4.4 15.2 1.0 N3 B:DA11 4.4 9.4 1.0 H3 A:DT6 4.5 11.3 1.0 H73 A:DT3 4.5 12.3 1.0 N1 B:DA11 4.5 10.7 1.0 H3 B:DT16 4.5 9.6 1.0 N3 A:DA1 4.5 7.2 1.0 N1 B:DA15 4.5 6.8 1.0 N3 A:DA5 4.5 5.9 1.0 H73 B:DT17 4.5 25.6 1.0 N3 B:DA15 4.6 7.2 1.0 H3 B:DT12 4.6 13.3 1.0 N1 A:DA5 4.6 5.5 1.0 N3 A:DT2 4.6 10.1 1.0 N3 A:DT6 4.6 7.5 1.0 N1 A:DA1 4.7 7.9 1.0 C1' B:DT12 4.7 7.5 1.0 N3 B:DT16 4.7 6.4 1.0 C1' B:DT16 4.7 8.1 1.0 N3 B:DT12 4.7 8.9 1.0 C1' A:DT6 4.7 7.5 1.0 N1 A:DT2 4.8 9.4 1.0 C1' A:DT2 4.8 9.0 1.0 N1 A:DT6 4.8 7.3 1.0 N1 B:DT12 4.8 7.5 1.0 N1 B:DT16 4.8 7.3 1.0 H71 A:DT7 4.9 18.6 1.0 C7 A:DT7 5.0 12.4 1.0

S.A.Salisbury, S.E.Wilson, H.R.Powell, O.Kennard, P.Lubini, G.M.Sheldrick, N.Escaja, E.Alazzouzi, A.Grandas, E.Pedroso. The Bi-Loop, A New General Four-Stranded Dna Motif. Proc.Natl.Acad.Sci.Usa V. 94 5515 1997.
ISSN: ISSN 0027-8424
PubMed: 9159103
DOI: 10.1073/PNAS.94.11.5515