Calcium in PDB 6uwg: Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site

The structure of Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site, PDB code: 6uwg was solved by R.Werther, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.43 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.324, 73.516, 163.526, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.1

The binding sites of Calcium atom in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site (pdb code 6uwg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site, PDB code: 6uwg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:21.9 occ:1.00 O A:HOH541 2.3 22.2 1.0 OP1 B:DC14 2.3 23.7 1.0 OP1 C:DA16 2.4 20.1 1.0 O A:ALA21 2.4 21.6 1.0 OD1 A:ASP178 2.5 23.2 1.0 O A:HOH517 2.6 18.8 1.0 OD2 A:ASP178 2.8 23.4 1.0 CG A:ASP178 3.0 22.4 1.0 C A:ALA21 3.3 22.0 1.0 CA A:CA404 3.3 21.4 0.6 CA A:ALA21 3.7 21.4 1.0 P C:DA16 3.7 23.8 1.0 P B:DC14 3.8 23.3 1.0 C5' C:DA16 4.0 20.6 1.0 O5' C:DA16 4.2 21.1 1.0 OE1 A:GLN204 4.3 25.4 1.0 N A:GLU22 4.4 21.3 1.0 C5' B:DC14 4.4 21.9 1.0 CB A:ALA21 4.4 23.6 1.0 C4' B:DC14 4.4 23.6 1.0 O A:ASP20 4.5 23.9 1.0 CB A:ASP178 4.5 21.5 1.0 O3' C:DT15 4.5 24.0 1.0 HO2 B:EDO102 4.6 31.9 1.0 OP2 B:DC14 4.6 25.3 1.0 NE2 A:GLN204 4.6 19.7 1.0 O3' B:DT13 4.6 22.3 1.0 O5' B:DC14 4.6 21.5 1.0 O A:HOH512 4.7 24.2 1.0 OP2 C:DA16 4.8 22.0 1.0 N A:ALA21 4.8 20.3 1.0 O3' B:DC14 4.9 23.7 1.0 CA A:GLU22 4.9 21.9 1.0 CD A:GLN204 4.9 24.6 1.0 O2 B:EDO102 5.0 26.6 1.0

Calcium binding site 2 out of 4 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:24.6 occ:1.00 OE1 A:GLU22 2.3 21.2 1.0 OP2 B:DA15 2.4 24.7 1.0 O A:GLY177 2.4 22.7 1.0 O C:HOH102 2.5 28.1 1.0 O A:HOH550 2.6 27.7 1.0 O A:HOH543 2.6 27.9 1.0 CD A:GLU22 3.4 21.0 1.0 C A:GLY177 3.4 22.4 1.0 CA A:CA404 3.5 21.4 0.6 P B:DA15 3.6 24.7 1.0 CA A:GLY177 4.0 23.8 1.0 O B:HOH212 4.0 32.2 1.0 O5' B:DA15 4.1 25.9 1.0 OE2 A:GLU22 4.1 21.2 1.0 C5' B:DA15 4.1 25.9 1.0 OP1 B:DA15 4.3 23.2 1.0 CG A:GLU22 4.4 20.9 1.0 OP1 C:DT15 4.4 21.9 1.0 N A:ASP178 4.6 21.4 1.0 O A:HOH539 4.6 28.6 1.0 O A:SER176 4.6 25.0 1.0 OD2 A:ASP178 4.7 23.4 1.0 O3' B:DC14 4.8 23.7 1.0 CA A:ASP178 4.9 22.1 1.0 C4' B:DA15 4.9 27.7 1.0

Calcium binding site 3 out of 4 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:23.6 occ:1.00 OP2 C:DA16 2.3 22.0 1.0 OE2 A:GLU22 2.3 21.2 1.0 O A:HOH518 2.3 19.7 1.0 O A:THR48 2.3 25.0 1.0 OP1 C:DT15 2.3 21.9 1.0 O C:HOH112 2.4 20.2 1.0 P C:DT15 3.4 23.6 1.0 CD A:GLU22 3.5 21.0 1.0 C A:THR48 3.5 27.2 1.0 P C:DA16 3.7 23.8 1.0 OP2 C:DT15 3.8 23.5 1.0 O5' C:DT15 3.9 26.0 1.0 O C:HOH102 4.0 28.1 1.0 OE1 A:GLU22 4.0 21.2 1.0 CA A:THR48 4.3 25.7 1.0 N A:THR48 4.3 25.0 1.0 CB A:THR48 4.5 25.7 1.0 O A:GLU22 4.5 23.4 1.0 C3' C:DT15 4.5 24.4 1.0 CD2 A:LEU49 4.5 25.1 1.0 C5' C:DT15 4.5 24.9 1.0 OP1 C:DA16 4.5 20.1 1.0 O3' C:DT15 4.5 24.0 1.0 N A:LEU49 4.6 26.6 1.0 O A:HOH535 4.6 26.0 1.0 O5' C:DA16 4.6 21.1 1.0 CA A:CA404 4.7 21.4 0.6 CG A:GLU22 4.7 20.9 1.0 CB A:GLU22 4.7 20.5 1.0 C8 C:DA16 4.7 25.1 1.0 N7 C:DA16 4.7 26.8 1.0 O3' C:DA14 4.8 27.6 1.0 CA A:LEU49 4.8 28.9 1.0 CA A:GLU22 4.8 21.9 1.0

Calcium binding site 4 out of 4 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Engineered Variant of I-Onui Meganuclease with Improved Thermostability and E178D Mutation at Catalytic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:21.4 occ:0.57 OD2 A:ASP178 2.1 23.4 1.0 OP1 C:DA16 2.3 20.1 1.0 OP2 B:DA15 2.4 24.7 1.0 OE1 A:GLU22 2.4 21.2 1.0 O A:ALA21 2.9 21.6 1.0 CD A:GLU22 3.1 21.0 1.0 O3' B:DC14 3.2 23.7 1.0 CA A:CA401 3.3 21.9 1.0 P C:DA16 3.3 23.8 1.0 CG A:ASP178 3.3 22.4 1.0 P B:DA15 3.4 24.7 1.0 CA A:CA402 3.5 24.6 1.0 O A:GLY177 3.6 22.7 1.0 OE2 A:GLU22 3.6 21.2 1.0 OP2 C:DA16 3.6 22.0 1.0 O3' C:DT15 3.8 24.0 1.0 C A:GLY177 3.9 22.4 1.0 OD1 A:ASP178 4.0 23.2 1.0 O5' B:DA15 4.0 25.9 1.0 CG A:GLU22 4.0 20.9 1.0 C A:ALA21 4.0 22.0 1.0 C3' B:DC14 4.1 25.0 1.0 CA A:ASP178 4.3 22.1 1.0 N A:ASP178 4.3 21.4 1.0 CB A:ASP178 4.4 21.5 1.0 C4' B:DC14 4.6 23.6 1.0 CA A:GLY177 4.6 23.8 1.0 OP1 B:DA15 4.7 23.2 1.0 OP1 B:DC14 4.7 23.7 1.0 CA A:CA403 4.7 23.6 1.0 O A:HOH541 4.7 22.2 1.0 O C:HOH102 4.7 28.1 1.0 CA A:GLU22 4.7 21.9 1.0 O5' C:DA16 4.7 21.1 1.0 C3' C:DT15 4.8 24.4 1.0 CB A:ALA21 4.8 23.6 1.0 N A:GLU22 4.9 21.3 1.0 CA A:ALA21 4.9 21.4 1.0 CB A:GLU22 4.9 20.5 1.0 OP1 C:DT15 5.0 21.9 1.0

R.Werther, B.L.Stoddard. Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein Dna-Binding Specificity To Be Published.