Sodium in PDB 7rce: Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions

The structure of Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions, PDB code: 7rce was solved by N.C.Ubilla-Rodriguez, R.A.Werther, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.74 / 2.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.935, 63.987, 165.24, 90, 90, 90
R / Rfree (%)	23.2 / 27.3

The structure of Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions (pdb code 7rce). 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 Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions, PDB code: 7rce:

Sodium binding site 1 out of 1 in the Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:77.3 occ:1.00 OP2 B:DA16 2.6 51.6 1.0 N A:PHE181 2.6 51.5 1.0 O A:PHE181 3.1 66.1 1.0 CA A:SER180 3.4 48.7 1.0 OD1 A:ASN298 3.4 73.6 1.0 C A:SER180 3.5 52.0 1.0 OG A:SER180 3.5 54.9 1.0 CA A:PHE181 3.6 58.2 1.0 CD A:LYS262 3.6 69.3 1.0 C A:PHE181 3.7 64.8 1.0 CE A:LYS262 3.7 64.5 1.0 O B:HOH101 3.7 53.3 1.0 P B:DA16 3.8 56.1 1.0 OD2 A:ASP265 3.9 76.0 1.0 CB A:PHE181 4.0 56.8 1.0 CB A:ASP265 4.0 75.7 1.0 CB A:SER180 4.1 51.9 1.0 CD2 A:PHE181 4.1 59.1 1.0 OP1 B:DA16 4.2 60.5 1.0 CG A:ASN298 4.2 79.9 1.0 ND2 A:ASN298 4.4 82.0 1.0 O5' B:DA16 4.5 62.1 1.0 CG A:ASP265 4.5 78.8 1.0 CG A:PHE181 4.5 56.9 1.0 N A:SER180 4.6 45.0 1.0 O A:SER180 4.7 52.5 1.0 O A:GLY179 4.8 52.2 1.0 N A:PHE182 4.9 66.0 1.0 CG A:LYS262 5.0 72.2 1.0

R.A.Werther, N.C.Ubilla-Rodriguez, A.T.Smiley, K.Havens, A.R.Lambert, B.L.Stoddard. Characterization of the Stepwise Engineering and Optimization of A Retargeted Dna Binding Protein and Gene-Editing Meganuclease To Be Published.