Calcium in PDB 7rcd: Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions

The structure of Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions, PDB code: 7rcd 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)	42.48 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.614, 64.457, 169.913, 90, 90, 90
R / Rfree (%)	23.5 / 27.7

The binding sites of Calcium atom in the Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions (pdb code 7rcd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions, PDB code: 7rcd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:37.2 occ:1.00 OP1 B:DC14 2.3 41.0 1.0 O A:ALA21 2.4 45.1 1.0 OP2 C:DC16 2.4 38.5 1.0 OD2 A:ASP178 2.4 33.7 1.0 O A:HOH502 2.5 37.2 1.0 O B:HOH102 2.7 45.7 1.0 OD1 A:ASP178 2.7 39.4 1.0 CG A:ASP178 2.9 37.9 1.0 C A:ALA21 3.2 38.2 1.0 CA A:ALA21 3.5 38.6 1.0 O A:HOH501 3.6 40.2 1.0 P B:DC14 3.7 39.1 1.0 P C:DC16 3.7 44.3 1.0 OE1 A:GLN204 4.1 39.0 1.0 CB A:ALA21 4.1 35.7 1.0 NE2 A:GLN204 4.2 29.3 1.0 O3' B:DC13 4.2 42.8 1.0 CB A:ASP178 4.3 38.4 1.0 OP1 C:DC16 4.4 44.0 1.0 C5' C:DC16 4.4 45.8 1.0 O5' C:DC16 4.4 47.0 1.0 OE1 A:GLU22 4.4 51.9 1.0 O A:ASP20 4.4 37.7 1.0 N A:GLU22 4.5 41.3 1.0 C4' B:DC14 4.5 46.2 1.0 C5' B:DC14 4.5 42.9 1.0 CD A:GLN204 4.5 38.7 1.0 OP2 B:DC14 4.7 40.6 1.0 O5' B:DC14 4.7 40.2 1.0 N A:ALA21 4.7 35.8 1.0 O3' C:DT15 4.9 41.2 1.0

Calcium binding site 2 out of 2 in the Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Second Stage Reengineered Variant of I-Onui Targeting Human PD1 Gene with Activity Enhancing Substitutions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:45.3 occ:1.00 OP1 C:DT15 2.3 38.8 1.0 OP2 B:DC15 2.4 42.4 1.0 OE2 A:GLU22 2.4 53.4 1.0 O A:GLY177 2.4 38.7 1.0 O A:HOH505 2.5 49.3 1.0 C A:GLY177 3.4 36.5 1.0 CD A:GLU22 3.4 43.0 1.0 P B:DC15 3.6 36.3 1.0 P C:DT15 3.8 39.6 1.0 CA A:GLY177 3.8 37.5 1.0 O A:HOH501 3.8 40.2 1.0 OE1 A:GLU22 3.9 51.9 1.0 OP1 B:DC15 4.2 41.5 1.0 C5' B:DC15 4.3 40.1 1.0 O5' B:DC15 4.3 41.4 1.0 O A:SER176 4.4 44.8 1.0 O3' C:DA14 4.4 42.8 1.0 C5' C:DT15 4.5 41.0 1.0 N A:ASP178 4.5 40.8 1.0 NZ A:LYS262 4.6 42.1 1.0 CG A:GLU22 4.6 48.5 1.0 O5' C:DT15 4.7 40.8 1.0 OP2 C:DT15 4.7 58.1 1.0 C4' C:DT15 4.7 44.7 1.0 O3' B:DC14 4.8 39.4 1.0 N A:GLY177 4.9 35.3 1.0 CA A:ASP178 4.9 37.5 1.0 OD1 A:ASP178 4.9 39.4 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.