Sodium in PDB 3gjl: Crystal Structure of A Dna Duplex Containing 7,8- Dihydropyridol[2,3-D]Pyrimidin-2-One

The structure of Crystal Structure of A Dna Duplex Containing 7,8- Dihydropyridol[2,3-D]Pyrimidin-2-One, PDB code: 3gjl was solved by A.Takenaka, E.C.M.Juan, S.Shimizu, T.Haraguchi, M.Xiao, T.Kurose, A.Ohkubo, M.Sekine, T.Shibata, C.L.Millington, D.M.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.34 / 1.92
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	26.477, 26.477, 98.958, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 26.4

The binding sites of Sodium atom in the Crystal Structure of A Dna Duplex Containing 7,8- Dihydropyridol[2,3-D]Pyrimidin-2-One (pdb code 3gjl). 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 A Dna Duplex Containing 7,8- Dihydropyridol[2,3-D]Pyrimidin-2-One, PDB code: 3gjl:

Sodium binding site 1 out of 1 in the Crystal Structure of A Dna Duplex Containing 7,8- Dihydropyridol[2,3-D]Pyrimidin-2-One


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 A Dna Duplex Containing 7,8- Dihydropyridol[2,3-D]Pyrimidin-2-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:5.5 occ:0.50 OP1 B:DG12 1.9 23.4 1.0 P B:DG12 3.2 21.5 1.0 O3' B:DC11 3.7 19.2 1.0 OP2 B:DG12 4.0 22.6 1.0 O5' B:DG12 4.4 23.0 1.0 C5' B:DG12 4.8 17.7 1.0 O B:HOH32 4.8 44.0 1.0

A.Takenaka, E.C.M.Juan, S.Shimizu, T.Haraguchi, M.Xiao, T.Kurose, A.Ohkubo, M.Sekine, T.Shibata, C.M.Millington, D.M.William. Insights Into the Stabilizing Contributions of Bicyclic Cytosine Analogues: Crystal Structures of Dna Duplexes Containing 7,8-Dihydropyridol[2,3-D]Pyrimidin-2-One To Be Published.