Sodium in PDB 1uhy: Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex

The structure of Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex, PDB code: 1uhy was solved by J.Kondo, S.I.Umeda, K.Fujita, T.Sunami, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.87 / 1.70
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	37.000, 37.000, 65.300, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 23.9

The structure of Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex (pdb code 1uhy). 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 D(Gcgatagc): the Base-Intercalated Duplex, PDB code: 1uhy:

Sodium binding site 1 out of 1 in the Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex


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 D(Gcgatagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:22.1 occ:1.00 O A:HOH49 2.1 47.5 1.0 O A:HOH63 2.2 40.3 1.0 O A:HOH44 2.2 39.9 1.0 O A:HOH48 2.2 41.2 1.0 O A:HOH39 2.2 51.2 1.0 O A:HOH67 2.2 45.1 1.0 O A:HOH53 4.2 35.4 1.0 O6 A:DG7 4.2 15.8 1.0 O A:HOH22 4.3 36.0 1.0 N7 A:DG7 4.4 17.2 1.0 O A:HOH62 4.7 68.3 1.0 O A:HOH10 4.8 27.0 1.0 O A:HOH32 5.0 41.3 1.0

J.Kondo, S.I.Umeda, K.Fujita, T.Sunami, A.Takenaka. X-Ray Analyses of D(Gcgaxagc) Containing G and T at X: the Base-Intercalated Duplex Is Still Stable Even in Point Mutants at the Fifth Residue. J.Synchrotron Radiat. V. 11 117 2004.
ISSN: ISSN 0909-0495
PubMed: 14646150
DOI: 10.1107/S0909049503023562