Calcium in PDB 6uwj: 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: 6uwj 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)	48.99 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.288, 62.586, 157.405, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.4

The binding sites of Calcium atom in the Intermediate Engineered Variant of I-Onui Meganuclease with Improved Thermostability and Partially Altered Specificity (pdb code 6uwj). 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: 6uwj:
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:20.3 occ:1.00 OP1 B:DC14 2.2 23.2 1.0 OP1 C:DA16 2.3 19.3 1.0 O A:ALA21 2.4 19.5 1.0 OD2 A:ASP178 2.4 18.9 1.0 O A:HOH565 2.5 24.8 1.0 O A:HOH511 2.5 19.9 1.0 OD1 A:ASP178 2.7 19.3 1.0 CG A:ASP178 2.9 19.7 1.0 C A:ALA21 3.3 19.3 1.0 O B:HOH101 3.4 17.0 1.0 CA A:ALA21 3.7 18.4 1.0 P C:DA16 3.7 21.7 1.0 P B:DC14 3.7 23.8 1.0 C5' C:DA16 3.9 20.8 1.0 O5' C:DA16 4.1 24.0 1.0 C5' B:DC14 4.2 23.7 1.0 OE1 A:GLN204 4.2 24.0 1.0 O A:HOH533 4.4 24.8 1.0 CB A:ALA21 4.4 19.2 1.0 C4' B:DC14 4.4 22.4 1.0 N A:GLU22 4.4 17.8 1.0 CB A:ASP178 4.4 20.1 1.0 O A:ASP20 4.5 18.7 1.0 O5' B:DC14 4.5 22.1 1.0 O3' C:DT15 4.5 22.4 1.0 O3' B:DT13 4.5 24.2 1.0 OP2 B:DC14 4.5 24.4 1.0 NE2 A:GLN204 4.5 19.2 1.0 OP2 C:DA16 4.8 20.9 1.0 CD A:GLN204 4.8 23.0 1.0 O A:HOH516 4.8 21.6 1.0 O3' B:DC14 4.8 23.5 1.0 N A:ALA21 4.9 18.6 1.0 CA A:GLU22 4.9 18.2 1.0 C3' B:DC14 5.0 21.8 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:20.4 occ:1.00 OP2 B:DG15 2.3 22.3 1.0 OE2 A:GLU22 2.3 20.0 1.0 O A:HOH572 2.3 28.4 1.0 O C:HOH204 2.4 25.6 1.0 O A:HOH553 2.4 27.4 1.0 O A:GLY177 2.5 22.6 1.0 CD A:GLU22 3.4 21.9 1.0 O B:HOH106 3.4 30.3 1.0 O B:HOH101 3.4 17.0 1.0 C A:GLY177 3.5 20.3 1.0 P B:DG15 3.5 20.5 1.0 CA A:GLY177 4.0 20.5 1.0 OE1 A:GLU22 4.0 19.4 1.0 OP1 B:DG15 4.1 21.4 1.0 O5' B:DG15 4.2 19.9 1.0 C5' B:DG15 4.3 21.2 1.0 OP1 C:DT15 4.3 20.5 1.0 CG A:GLU22 4.4 20.5 1.0 O A:HOH556 4.4 27.2 1.0 O A:SER176 4.6 24.5 1.0 N A:ASP178 4.6 20.1 1.0 O3' B:DC14 4.7 23.5 1.0 O A:HOH514 4.8 34.1 1.0 OD1 A:ASP178 4.8 19.3 1.0 CA A:ASP178 5.0 19.0 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 C:Ca101 b:20.8 occ:1.00 OP2 C:DA16 2.3 20.9 1.0 OE1 A:GLU22 2.3 19.4 1.0 OP1 C:DT15 2.4 20.5 1.0 O A:THR48 2.4 19.1 1.0 O C:HOH216 2.4 21.1 1.0 O A:HOH508 2.4 17.8 1.0 P C:DT15 3.4 23.1 1.0 CD A:GLU22 3.5 21.9 1.0 C A:THR48 3.6 19.8 1.0 P C:DA16 3.8 21.7 1.0 OP2 C:DT15 3.8 21.5 1.0 O5' C:DT15 4.0 20.6 1.0 OE2 A:GLU22 4.1 20.0 1.0 O C:HOH204 4.1 25.6 1.0 N A:THR48 4.3 17.2 1.0 CA A:THR48 4.3 20.6 1.0 O A:GLU22 4.3 20.1 1.0 O A:HOH551 4.4 21.8 1.0 CD2 A:LEU49 4.4 20.1 1.0 C3' C:DT15 4.5 22.1 1.0 CB A:THR48 4.5 21.0 1.0 C5' C:DT15 4.5 24.5 1.0 O3' C:DT15 4.6 22.4 1.0 OP1 C:DA16 4.6 19.3 1.0 N A:LEU49 4.6 18.9 1.0 C8 C:DA16 4.6 21.9 1.0 O B:HOH101 4.6 17.0 1.0 O5' C:DA16 4.6 24.0 1.0 CG A:GLU22 4.7 20.5 1.0 CB A:GLU22 4.7 18.1 1.0 N7 C:DA16 4.7 22.9 1.0 CA A:GLU22 4.7 18.2 1.0 O3' C:DA14 4.7 25.0 1.0 CA A:LEU49 4.8 19.2 1.0 O A:HOH516 4.9 21.6 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:Ca102 b:30.7 occ:1.00 O C:HOH222 2.4 29.7 1.0 O B:HOH125 2.4 29.2 1.0 O C:HOH228 2.5 33.4 1.0 N2 C:DG21 4.5 20.9 1.0 O C:HOH208 4.6 26.1 1.0 O4' C:DA22 4.7 23.4 1.0 O2 B:DC6 4.8 26.1 1.0 C4' C:DA22 4.8 26.2 1.0 C5' B:DA7 4.9 27.6 1.0 N3 C:DG21 5.0 24.0 1.0 O4' B:DA7 5.0 26.6 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.