Calcium 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
Sodium	(Na)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions, PDB code: 7rcf:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca503 b:17.8 occ:1.00 OP2 B:DC15 2.3 16.8 1.0 O B:HOH511 2.3 17.7 1.0 OP1 C:DT15 2.3 16.8 1.0 OE2 A:GLU22 2.3 23.7 1.0 O A:HOH628 2.4 23.9 1.0 O A:GLY177 2.4 18.1 1.0 C A:GLY177 3.4 17.0 1.0 CA A:CA505 3.5 30.4 1.0 CD A:GLU22 3.6 24.2 1.0 P B:DC15 3.6 16.5 1.0 P C:DT15 3.8 17.1 1.0 O B:HOH503 3.8 19.0 1.0 CA A:GLY177 3.9 16.2 1.0 O5' B:DC15 4.1 18.3 1.0 C5' B:DC15 4.2 18.9 1.0 OE1 A:GLU22 4.3 29.1 1.0 OP1 B:DC15 4.3 17.7 1.0 O3' C:DA14 4.4 16.5 1.0 C5' C:DT15 4.4 16.7 1.0 C4' C:DT15 4.5 20.6 1.0 O A:SER176 4.5 14.3 1.0 N A:ASP178 4.6 16.0 1.0 CG A:GLU22 4.6 21.9 1.0 O5' C:DT15 4.6 16.1 1.0 OP2 C:DT15 4.7 18.6 1.0 O3' B:DC14 4.7 19.0 1.0 OD1 A:ASP178 5.0 13.6 1.0 CA A:ASP178 5.0 13.6 1.0

Calcium binding site 2 out of 3 in the Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:13.5 occ:1.00 OP2 C:DC16 2.2 14.9 1.0 OP1 B:DC14 2.3 13.1 1.0 O A:ALA21 2.3 15.6 1.0 O A:HOH625 2.3 15.1 1.0 OD2 A:ASP178 2.4 11.5 1.0 O C:HOH116 2.5 17.6 1.0 OD1 A:ASP178 2.8 13.6 1.0 CG A:ASP178 3.0 15.4 1.0 C A:ALA21 3.3 15.0 1.0 P C:DC16 3.5 18.1 1.0 P B:DC14 3.7 13.9 1.0 CA A:ALA21 3.7 14.7 1.0 CA A:CA505 3.8 30.4 1.0 O3' B:DC13 4.1 15.0 1.0 O5' C:DC16 4.2 17.0 1.0 OE1 A:GLN204 4.2 12.2 1.0 OP1 C:DC16 4.2 16.1 1.0 C5' C:DC16 4.2 17.6 1.0 O A:HOH649 4.2 23.0 1.0 OE1 A:GLU22 4.3 29.1 1.0 NE2 A:GLN204 4.4 11.9 1.0 C4' B:DC14 4.4 15.4 1.0 CB A:ALA21 4.4 13.0 1.0 CB A:ASP178 4.5 12.8 1.0 N A:GLU22 4.5 15.1 1.0 C5' B:DC14 4.6 13.3 1.0 O A:ASP20 4.6 16.0 1.0 OP2 B:DC14 4.6 14.3 1.0 CD A:GLN204 4.7 15.7 1.0 O3' C:DT15 4.7 16.3 1.0 O5' B:DC14 4.7 14.6 1.0 CA A:GLU22 5.0 18.7 1.0 N A:ALA21 5.0 13.5 1.0

Calcium binding site 3 out of 3 in the Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fourth Stage Reengineered Variant of I-Onui with Stability Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:30.4 occ:1.00 OD1 A:ASP178 2.3 13.6 1.0 OP2 B:DC15 2.4 16.8 1.0 OE1 A:GLU22 2.4 29.1 1.0 OP2 C:DC16 2.5 14.9 1.0 OE2 A:GLU22 2.7 23.7 1.0 CD A:GLU22 2.8 24.2 1.0 O3' C:DT15 2.8 16.3 1.0 O3' B:DC14 2.9 19.0 1.0 P B:DC15 3.2 16.5 1.0 P C:DC16 3.3 18.1 1.0 O A:GLY177 3.5 18.1 1.0 CA A:CA503 3.5 17.8 1.0 CG A:ASP178 3.6 15.4 1.0 C3' C:DT15 3.6 18.3 1.0 CA A:CA504 3.8 13.5 1.0 C3' B:DC14 3.9 18.0 1.0 C4' C:DT15 3.9 20.6 1.0 C A:GLY177 4.0 17.0 1.0 O A:ALA21 4.0 15.6 1.0 O5' B:DC15 4.1 18.3 1.0 CG A:GLU22 4.1 21.9 1.0 O5' C:DC16 4.2 17.0 1.0 CA A:ASP178 4.3 13.6 1.0 C4' B:DC14 4.3 15.4 1.0 OD2 A:ASP178 4.4 11.5 1.0 OP1 B:DC15 4.4 17.7 1.0 N A:ASP178 4.4 16.0 1.0 OP1 C:DC16 4.4 16.1 1.0 CB A:ASP178 4.5 12.8 1.0 C A:ALA21 4.7 15.0 1.0 OP1 C:DT15 4.7 16.8 1.0 C5' C:DT15 4.7 16.7 1.0 CA A:GLY177 4.8 16.2 1.0 OP1 B:DC14 4.9 13.1 1.0 O B:HOH504 4.9 23.2 1.0 CA A:GLU22 5.0 18.7 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.