Sodium in PDB 7rcf: Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions

The structure of Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions, PDB code: 7rcf 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)	37.38 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.55, 64.055, 171.296, 90, 90, 90
R / Rfree (%)	19 / 22.9

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

Chlorine	(Cl)	1 atom
Calcium	(Ca)	3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:34.1 occ:1.00 CL A:CL506 2.7 38.8 1.0 O A:HOH642 2.8 25.2 1.0 OH A:TYR218 2.8 15.6 1.0 CZ A:TYR218 3.3 20.3 1.0 CE2 A:TYR218 3.3 14.8 1.0 CG2 A:VAL252 3.7 13.2 1.0 CG1 A:VAL252 4.2 15.2 1.0 ND2 A:ASN256 4.2 14.6 1.0 O A:HOH654 4.3 27.9 1.0 CE1 A:TYR218 4.4 18.6 1.0 CD2 A:TYR218 4.4 15.2 1.0 CB A:VAL252 4.5 14.7 1.0 CA A:GLY168 4.7 14.3 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.