Calcium in PDB 6uwh: Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity

The structure of Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity, PDB code: 6uwh 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)	27.23 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.890, 72.985, 163.574, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25

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

Calcium binding site 1 out of 4 in the Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:28.2 occ:1.00 O C:HOH207 2.2 29.4 1.0 OP1 B:DC14 2.3 28.3 1.0 OD2 A:ASP178 2.3 28.3 1.0 OP1 C:DA16 2.3 30.1 1.0 O A:ALA21 2.4 27.6 1.0 O A:HOH512 2.5 26.0 1.0 OD1 A:ASP178 2.9 29.8 1.0 CG A:ASP178 3.0 30.6 1.0 C A:ALA21 3.2 28.2 1.0 O A:HOH501 3.3 19.7 1.0 CA A:ALA21 3.5 27.9 1.0 P C:DA16 3.7 28.4 1.0 P B:DC14 3.8 26.3 1.0 C5' C:DA16 4.0 31.1 1.0 O A:HOH506 4.0 29.0 1.0 O5' C:DA16 4.2 28.6 1.0 CB A:ALA21 4.2 24.6 1.0 N A:GLU22 4.2 30.4 1.0 OE1 A:GLN204 4.3 28.4 1.0 C5' B:DC14 4.3 29.3 1.0 O A:ASP20 4.4 30.5 1.0 CB A:ASP178 4.4 27.1 1.0 C4' B:DC14 4.5 31.6 1.0 O3' C:DT15 4.5 32.1 1.0 O5' B:DC14 4.6 27.9 1.0 O3' B:DT13 4.6 26.6 1.0 OP2 B:DC14 4.6 32.3 1.0 N A:ALA21 4.7 25.9 1.0 OP2 C:DA16 4.7 26.6 1.0 O A:HOH517 4.7 32.4 1.0 NE2 A:GLN204 4.8 25.2 1.0 CA A:GLU22 4.8 29.9 1.0 CD A:GLN204 4.9 33.1 1.0

Calcium binding site 2 out of 4 in the Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:27.3 occ:1.00 OE1 A:GLU22 2.2 27.2 1.0 O C:HOH204 2.3 34.4 1.0 OP2 B:DG15 2.3 26.0 1.0 O A:GLY177 2.4 24.4 1.0 O A:HOH521 2.5 29.1 1.0 O A:HOH510 2.5 29.6 1.0 O B:HOH102 2.8 38.0 1.0 CD A:GLU22 3.3 29.0 1.0 P B:DG15 3.4 26.7 1.0 O A:HOH501 3.5 19.7 1.0 C A:GLY177 3.5 25.6 1.0 OP1 B:DG15 3.8 28.0 1.0 OE2 A:GLU22 3.9 26.6 1.0 CA A:GLY177 4.0 26.1 1.0 O5' B:DG15 4.1 29.9 1.0 OP1 C:DT15 4.2 28.2 1.0 C5' B:DG15 4.2 27.9 1.0 CG A:GLU22 4.4 26.8 1.0 OD1 A:ASP178 4.5 29.8 1.0 O A:SER176 4.6 28.4 1.0 N A:ASP178 4.6 23.5 1.0 O3' B:DC14 4.7 29.5 1.0 C4' B:DG15 4.9 32.2 1.0 CD2 A:LEU49 4.9 33.8 1.0 CA A:ASP178 5.0 26.8 1.0

Calcium binding site 3 out of 4 in the Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:59.6 occ:1.00 OP2 B:DC18 2.2 44.7 1.0 NZ A:LYS294 2.9 32.9 1.0 C2' B:DC17 3.1 36.6 1.0 C3' B:DC17 3.2 43.5 1.0 CE A:LYS294 3.3 29.5 1.0 CZ A:PHE182 3.3 31.8 1.0 P B:DC18 3.5 47.2 1.0 C5' B:DC18 3.7 45.6 1.0 CE1 A:PHE182 3.7 28.7 1.0 O3' B:DC17 3.8 42.5 1.0 O5' B:DC18 4.1 46.3 1.0 CE2 A:PHE182 4.4 35.6 1.0 O5' B:DC17 4.5 31.5 1.0 C4' B:DC17 4.5 38.9 1.0 C1' B:DC17 4.5 34.6 1.0 O A:VAL183 4.6 29.1 1.0 O B:HOH103 4.7 33.0 1.0 CD A:LYS294 4.8 32.4 1.0 OP1 B:DC18 4.8 50.2 1.0 O4' B:DC17 4.9 32.9 1.0 C6 B:DC18 4.9 36.2 1.0

Calcium binding site 4 out of 4 in the Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:28.5 occ:1.00 OP2 C:DA16 2.3 26.6 1.0 O A:HOH514 2.3 28.4 1.0 OP1 C:DT15 2.4 28.2 1.0 O C:HOH201 2.4 26.8 1.0 O A:THR48 2.4 25.7 1.0 OE2 A:GLU22 2.4 26.6 1.0 P C:DT15 3.4 29.7 1.0 C A:THR48 3.6 28.6 1.0 CD A:GLU22 3.6 29.0 1.0 OP2 C:DT15 3.7 28.2 1.0 P C:DA16 3.8 28.4 1.0 O5' C:DT15 3.9 34.4 1.0 O C:HOH204 4.0 34.4 1.0 OE1 A:GLU22 4.1 27.2 1.0 CA A:THR48 4.4 31.1 1.0 CD2 A:LEU49 4.4 33.8 1.0 N A:THR48 4.4 27.3 1.0 C3' C:DT15 4.5 32.2 1.0 C5' C:DT15 4.5 26.1 1.0 O A:GLU22 4.5 33.4 1.0 CB A:THR48 4.5 29.4 1.0 O3' C:DT15 4.5 32.1 1.0 OP1 C:DA16 4.6 30.1 1.0 N A:LEU49 4.6 33.3 1.0 O A:HOH501 4.6 19.7 1.0 O A:HOH513 4.6 32.7 1.0 O5' C:DA16 4.6 28.6 1.0 C8 C:DA16 4.7 33.0 1.0 CA A:GLU22 4.7 29.9 1.0 O3' C:DA14 4.8 30.2 1.0 CB A:GLU22 4.8 29.5 1.0 N7 C:DA16 4.8 30.7 1.0 CG A:GLU22 4.8 26.8 1.0 CA A:LEU49 4.8 32.4 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.