Sodium in PDB 1dcr: Crystal Structure of Dna Sheared Tandem G-A Base Pairs

The structure of Crystal Structure of Dna Sheared Tandem G-A Base Pairs, PDB code: 1dcr was solved by Y.-G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	20.950, 61.860, 68.490, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 26.6

The structure of Crystal Structure of Dna Sheared Tandem G-A Base Pairs also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Magnesium	(Mg)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Dna Sheared Tandem G-A Base Pairs (pdb code 1dcr). 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 Crystal Structure of Dna Sheared Tandem G-A Base Pairs, PDB code: 1dcr:

Sodium binding site 1 out of 1 in the Crystal Structure of Dna Sheared Tandem G-A Base Pairs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dna Sheared Tandem G-A Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:Na25 b:55.9 occ:1.00 OP2 B:BRU16 2.1 34.2 1.0 O5' B:BRU16 2.5 38.2 1.0 O B:HOH1014 2.9 37.6 1.0 P B:BRU16 2.9 36.4 1.0 C2' B:DA15 3.5 28.2 1.0 O B:HOH1070 3.8 49.9 0.5 C5' B:BRU16 3.9 31.3 1.0 C2' B:BRU16 3.9 30.4 1.0 O3' B:DA15 3.9 28.7 1.0 C6 B:BRU16 4.0 17.3 1.0 C3' B:DA15 4.1 34.8 1.0 OP1 B:BRU16 4.1 33.0 1.0 C3' B:BRU16 4.1 21.8 1.0 C4' B:BRU16 4.3 34.0 1.0 O4' B:BRU16 4.4 34.5 1.0 BR B:BRU16 4.6 34.1 1.0 C1' B:BRU16 4.6 24.2 1.0 C1' B:DA15 4.7 23.5 1.0 C5 B:BRU16 4.7 32.3 1.0 N7 B:DG17 4.8 29.9 1.0 N1 B:BRU16 4.8 25.9 1.0 O6 B:DG17 4.8 35.9 1.0 O B:HOH1010 4.9 40.7 1.0

Y.G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, A.H.Wang. Structure and Recognition of Sheared Tandem G X A Base Pairs Associated with Human Centromere Dna Sequence at Atomic Resolution. Biochemistry V. 38 16452 1999.
ISSN: ISSN 0006-2960
PubMed: 10600106
DOI: 10.1021/BI9914614