Sodium in PDB 4r49: Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex

The structure of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex, PDB code: 4r49 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)	34.25 / 1.28
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	23.263, 33.604, 36.820, 103.32, 101.02, 109.78
R / Rfree (%)	21.7 / 26

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

Calcium

(Ca)

7 atoms

The binding sites of Sodium atom in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex (pdb code 4r49). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex, PDB code: 4r49:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Racemic Crystal Structure of A Calcium-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 Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:26.2 occ:1.00 OP2 A:DT5 2.4 11.0 1.0 O A:HOH274 2.6 25.0 1.0 P A:DT5 3.8 9.2 1.0 O A:HOH280 3.8 37.0 1.0 O A:HOH279 3.8 34.1 1.0 O A:HOH205 4.2 15.1 1.0 C3' A:DG4 4.3 8.9 1.0 O A:HOH282 4.3 41.0 1.0 OP1 A:DT5 4.4 9.8 1.0 O3' A:DG4 4.4 8.2 1.0 O A:HOH276 4.4 26.9 1.0 O A:HOH263 4.6 20.4 0.5 O A:HOH271 4.6 18.4 1.0 O5' A:DT5 4.9 9.4 1.0 C2' A:DG4 5.0 9.5 1.0

Sodium binding site 2 out of 2 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:8.6 occ:0.49 OP1 B:DG4 2.2 14.9 1.0 O B:HOH238 2.2 30.6 0.7 O B:HOH225 2.4 16.3 0.8 P B:DG4 3.5 12.6 1.0 OP2 B:DG4 4.1 14.8 1.0 O B:HOH235 4.1 16.2 0.6 O5' B:DG4 4.2 10.8 1.0 O B:HOH260 4.4 30.5 1.0 C5' B:DG4 4.4 10.4 1.0 O3' B:DG3 4.6 11.6 1.0 O B:HOH242 4.6 19.4 0.6

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