Calcium 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:

Sodium

(Na)

1 atom

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca401 b:44.0 occ:1.00 OP1 B:DC14 2.2 47.1 1.0 O A:ALA21 2.4 41.9 1.0 OP2 C:DC16 2.4 41.4 1.0 O A:HOH504 2.4 33.5 1.0 OD2 A:ASP178 2.4 41.2 1.0 OD1 A:ASP178 2.8 42.5 1.0 CG A:ASP178 3.0 42.5 1.0 C A:ALA21 3.4 43.5 1.0 P B:DC14 3.5 39.0 1.0 P C:DC16 3.7 39.1 1.0 CA A:ALA21 3.7 43.4 1.0 CA A:CA403 3.9 67.2 1.0 O3' B:DC13 4.0 39.8 1.0 OE1 A:GLN204 4.2 47.0 1.0 C5' C:DC16 4.2 42.9 1.0 O5' C:DC16 4.2 44.8 1.0 NE2 A:GLN204 4.3 43.7 1.0 CB A:ALA21 4.4 41.5 1.0 OP1 C:DC16 4.4 47.1 1.0 OP2 B:DC14 4.4 52.2 1.0 C4' B:DC14 4.5 45.0 1.0 CB A:ASP178 4.5 45.0 1.0 C5' B:DC14 4.5 47.4 1.0 O A:ASP20 4.6 40.8 1.0 N A:GLU22 4.6 38.4 1.0 O5' B:DC14 4.6 43.2 1.0 OE1 A:GLU22 4.6 62.1 1.0 CD A:GLN204 4.6 48.1 1.0 O3' C:DT15 4.8 45.7 1.0 N A:ALA21 4.9 40.9 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:47.4 occ:1.00 OP2 B:DC15 2.2 43.6 1.0 O A:HOH506 2.3 37.9 1.0 OE2 A:GLU22 2.3 65.2 1.0 O A:GLY177 2.4 49.0 1.0 OP1 C:DT15 2.5 37.8 1.0 O A:HOH503 2.6 39.6 1.0 C A:GLY177 3.3 42.6 1.0 CD A:GLU22 3.4 59.4 1.0 CA A:CA403 3.5 67.2 1.0 P B:DC15 3.6 45.4 1.0 OE1 A:GLU22 3.8 62.1 1.0 CA A:GLY177 3.9 40.9 1.0 P C:DT15 3.9 42.0 1.0 C5' B:DC15 4.0 42.2 1.0 O5' B:DC15 4.1 40.9 1.0 NZ A:LYS262 4.2 65.4 1.0 O A:SER176 4.4 48.1 1.0 O3' C:DA14 4.4 48.4 1.0 OP1 B:DC15 4.4 48.6 1.0 N A:ASP178 4.5 47.4 1.0 C5' C:DT15 4.6 44.2 1.0 O3' B:DC14 4.7 42.6 1.0 CG A:GLU22 4.7 48.7 1.0 C4' C:DT15 4.7 42.4 1.0 O5' C:DT15 4.8 46.9 1.0 CA A:ASP178 4.8 50.0 1.0 OP2 C:DT15 4.9 58.7 1.0 OD1 A:ASP178 4.9 42.5 1.0 C4' B:DC15 4.9 48.1 1.0 N A:GLY177 5.0 40.5 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Third Stage Reengineered Variant of I-Onui with Specificity Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:67.2 occ:1.00 OP2 B:DC15 2.3 43.6 1.0 OD1 A:ASP178 2.3 42.5 1.0 OE1 A:GLU22 2.4 62.1 1.0 OP2 C:DC16 2.6 41.4 1.0 O3' B:DC14 2.7 42.6 1.0 O3' C:DT15 3.0 45.7 1.0 P B:DC15 3.0 45.4 1.0 CD A:GLU22 3.2 59.4 1.0 P C:DC16 3.4 39.1 1.0 OE2 A:GLU22 3.4 65.2 1.0 CA A:CA402 3.5 47.4 1.0 CG A:ASP178 3.5 42.5 1.0 C3' B:DC14 3.8 43.4 1.0 O A:GLY177 3.8 49.0 1.0 C3' C:DT15 3.8 44.0 1.0 CA A:CA401 3.9 44.0 1.0 O5' B:DC15 4.0 40.9 1.0 C A:GLY177 4.1 42.6 1.0 O A:ALA21 4.1 41.9 1.0 C4' C:DT15 4.1 42.4 1.0 CA A:ASP178 4.2 50.0 1.0 OP1 B:DC15 4.2 48.6 1.0 C4' B:DC14 4.2 45.0 1.0 N A:ASP178 4.3 47.4 1.0 O5' C:DC16 4.3 44.8 1.0 OD2 A:ASP178 4.4 41.2 1.0 CB A:ASP178 4.4 45.0 1.0 CG A:GLU22 4.4 48.7 1.0 OP1 C:DC16 4.5 47.1 1.0 OP1 C:DT15 4.6 37.8 1.0 C A:ALA21 4.7 43.5 1.0 CA A:GLY177 4.8 40.9 1.0 OP1 B:DC14 4.8 47.1 1.0 C5' C:DT15 4.9 44.2 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.