Sodium in PDB 9b8u: Crystal Structure of Crx-RET4 Oligonucleotide Complex

The structure of Crystal Structure of Crx-RET4 Oligonucleotide Complex, PDB code: 9b8u was solved by D.Srivastava, N.O.Artemyev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.67 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.597, 75.494, 97.229, 90, 120.25, 90
R / Rfree (%)	24.9 / 24.9

The structure of Crystal Structure of Crx-RET4 Oligonucleotide Complex also contains other interesting chemical elements:

Arsenic	(As)	2 atoms
Potassium	(K)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Crx-RET4 Oligonucleotide Complex (pdb code 9b8u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Crx-RET4 Oligonucleotide Complex, PDB code: 9b8u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Crx-RET4 Oligonucleotide Complex


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 Crx-RET4 Oligonucleotide Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Na101 b:67.3 occ:1.00 N7 G:DG30 2.5 64.7 1.0 O6 G:DG30 3.2 62.0 1.0 C5 G:DG30 3.3 64.0 1.0 N6 G:DA31 3.4 50.5 1.0 C8 G:DG30 3.5 69.2 1.0 C6 G:DG30 3.6 65.7 1.0 N7 G:DG29 3.9 70.4 1.0 C5 G:DG29 4.1 63.0 1.0 C8 G:DG29 4.3 72.3 1.0 C6 G:DG29 4.4 61.7 1.0 C6 G:DA31 4.4 63.0 1.0 O4 H:DT8 4.5 75.0 1.0 C4 G:DG30 4.5 63.2 1.0 C4 G:DG29 4.6 68.6 1.0 O6 G:DG29 4.6 74.4 1.0 N9 G:DG30 4.6 71.0 1.0 N9 G:DG29 4.7 76.6 1.0 N1 G:DG30 4.9 67.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Crx-RET4 Oligonucleotide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Crx-RET4 Oligonucleotide Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Na102 b:76.8 occ:1.00 OP2 G:DA20 2.9 86.1 1.0 O G:HOH208 3.7 61.3 1.0 P G:DA20 4.0 88.8 1.0 OP1 G:DA20 4.2 99.7 1.0 O D:HOH203 4.7 54.0 1.0 O3' G:DC19 4.7 78.9 1.0 C5' G:DC19 4.8 86.2 1.0 O5' G:DC19 4.8 84.1 1.0

D.Srivastava, N.O.Artemyev. Molecular Basis of Crx Homeodomain/Dna Binding and Stoichiometry at the RET4 Cis-Regulatory Element in Rhodopsin Promoter To Be Published.