Sodium in PDB 4r4d: Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex

The structure of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex, PDB code: 4r4d was solved by P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.54 / 1.29
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	31.610, 32.951, 46.250, 70.76, 80.77, 73.77
R / Rfree (%)	26.9 / 31.1

The structure of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Sodium atom in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex (pdb code 4r4d). 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 Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex, PDB code: 4r4d:

Sodium binding site 1 out of 1 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:8.6 occ:0.30 O C:HOH215 2.0 22.1 1.0 O C:HOH208 2.1 17.6 1.0 O D:HOH205 2.1 16.2 1.0 O4' C:DA6 4.2 23.6 0.5 N3 C:DA6 4.3 14.7 0.5 O4' C:DC7 4.3 14.9 0.5 N3 D:DA6 4.4 15.1 1.0 O D:HOH204 4.4 20.9 1.0 C2 D:DA6 4.4 15.1 1.0 O2 D:DC7 4.4 11.9 1.0 O2 C:DT5 4.6 16.8 1.0 C4' C:DA6 4.7 23.4 0.5 O4' D:DC7 4.8 12.6 1.0 O4' C:DC7 4.8 8.6 0.5 C1' D:DC7 4.8 12.9 1.0 O4' C:DA6 4.8 10.1 0.5 C1' C:DA6 4.8 16.5 0.5 N3 C:DA6 4.9 11.6 0.5 C4' C:DC7 4.9 15.2 0.5 C2 C:DA6 4.9 10.8 0.5 C5' C:DC7 5.0 18.6 0.5

P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc. Racemic Dna Crystallography. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25358289
DOI: 10.1002/ANIE.201409014