Calcium in PDB 6uwk: Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site

The structure of Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site, PDB code: 6uwk 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)	28.52 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.370, 62.635, 160.199, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.8

The binding sites of Calcium atom in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site (pdb code 6uwk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site, PDB code: 6uwk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration 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 Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:26.4 occ:1.00 OP1 B:DC14 2.2 31.2 1.0 O A:ALA21 2.2 27.7 1.0 OP1 C:DA16 2.3 30.3 1.0 OD2 A:ASP178 2.6 27.2 1.0 O A:HOH508 2.6 26.9 1.0 O A:HOH510 2.6 28.1 1.0 OD1 A:ASP178 2.7 28.6 1.0 CG A:ASP178 3.0 28.1 1.0 C A:ALA21 3.3 27.1 1.0 O A:HOH501 3.5 29.1 1.0 P C:DA16 3.6 30.1 1.0 CA A:ALA21 3.7 26.9 1.0 P B:DC14 3.7 30.0 1.0 C5' C:DA16 3.8 30.8 1.0 O5' C:DA16 4.0 30.2 1.0 OE1 A:GLN204 4.1 30.7 1.0 C5' B:DC14 4.2 30.8 1.0 O3' C:DT15 4.3 32.8 1.0 C4' B:DC14 4.4 31.4 1.0 O A:ASP20 4.4 26.5 1.0 N A:GLU22 4.4 26.3 1.0 CB A:ALA21 4.5 26.7 1.0 O3' B:DT13 4.5 31.2 1.0 O5' B:DC14 4.5 32.2 1.0 CB A:ASP178 4.5 27.6 1.0 OP2 B:DC14 4.6 31.1 1.0 OE1 A:GLU22 4.6 30.0 1.0 OP2 C:DA16 4.8 32.5 1.0 N A:ALA21 4.9 25.2 1.0 CD A:GLN204 4.9 30.2 1.0 NE2 A:GLN204 4.9 28.2 1.0 CA A:GLU22 4.9 26.9 1.0 O3' B:DC14 4.9 30.5 1.0

Calcium binding site 2 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration 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 Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:39.0 occ:1.00 OP1 B:DC6 2.4 32.9 1.0 O B:HOH109 2.4 33.0 1.0 O A:ILE69 2.6 31.0 1.0 O B:HOH108 2.8 32.2 1.0 O B:HOH107 3.0 36.3 1.0 P B:DC6 3.5 32.7 1.0 C A:ILE69 3.9 30.1 1.0 OP2 B:DC6 3.9 31.9 1.0 O5' B:DC6 4.3 31.6 1.0 N A:ILE69 4.5 30.8 1.0 CA A:ILE69 4.7 29.5 1.0 N A:ALA70 4.8 30.0 1.0 O3' B:DC5 4.8 31.2 1.0 CA A:ALA70 4.8 30.6 1.0 C5' B:DC6 4.9 31.3 1.0 CB A:ALA70 4.9 28.8 1.0

Calcium binding site 3 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration 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 Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:30.4 occ:1.00 OP2 B:DG15 2.4 30.3 1.0 O A:GLY177 2.4 28.3 1.0 O C:HOH102 2.4 31.8 1.0 O A:HOH512 2.5 31.0 1.0 OE1 A:GLU22 2.9 30.0 1.0 O A:HOH501 3.4 29.1 1.0 C A:GLY177 3.5 27.6 1.0 P B:DG15 3.6 30.2 1.0 CD A:GLU22 3.7 29.1 1.0 CA A:GLY177 4.0 27.6 1.0 C5' B:DG15 4.0 30.5 1.0 O5' B:DG15 4.1 31.3 1.0 OP1 B:DG15 4.1 32.2 1.0 OE2 A:GLU22 4.2 30.3 1.0 NZ A:LYS262 4.3 30.3 1.0 O A:SER176 4.4 27.1 1.0 OP1 C:DT15 4.5 34.2 1.0 N A:ASP178 4.7 27.6 1.0 CG A:GLU22 4.7 27.6 1.0 O3' B:DC14 4.8 30.5 1.0 OD1 A:ASP178 4.9 28.6 1.0 C4' B:DG15 4.9 31.7 1.0 CD2 A:LEU49 5.0 30.0 1.0 C5' C:DT15 5.0 34.5 1.0

Calcium binding site 4 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration 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 Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:37.0 occ:1.00 O A:GLY65 2.5 29.4 1.0 O A:HOH506 2.9 33.5 1.0 O A:HOH511 3.6 32.3 1.0 C A:GLY65 3.7 28.9 1.0 CG2 A:VAL66 4.3 28.6 1.0 CA A:GLY65 4.5 28.1 1.0 OD1 A:ASP86 4.6 30.8 1.0 N A:VAL66 4.6 28.5 1.0 CA A:VAL66 4.8 28.9 1.0

Calcium binding site 5 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:32.8 occ:1.00 OP2 C:DA16 2.2 32.5 1.0 OE2 A:GLU22 2.3 30.3 1.0 O C:HOH101 2.3 31.6 1.0 O A:HOH514 2.4 29.8 1.0 O A:THR48 2.4 30.8 1.0 OP2 C:DT15 3.2 34.3 1.0 O5' C:DT15 3.3 35.0 1.0 CD A:GLU22 3.5 29.1 1.0 P C:DT15 3.5 34.2 1.0 OP1 C:DT15 3.6 34.2 1.0 C A:THR48 3.6 30.7 1.0 P C:DA16 3.7 30.1 1.0 OE1 A:GLU22 4.1 30.0 1.0 C5' C:DT15 4.2 34.5 1.0 O C:HOH102 4.3 31.8 1.0 CA A:THR48 4.4 30.8 1.0 N7 C:DA16 4.4 34.0 1.0 C3' C:DT15 4.4 33.3 1.0 C8 C:DA16 4.4 32.7 1.0 CB A:THR48 4.4 30.9 1.0 N A:THR48 4.4 29.8 1.0 O3' C:DT15 4.5 32.8 1.0 OP1 C:DA16 4.5 30.3 1.0 CD2 A:LEU49 4.6 30.0 1.0 O5' C:DA16 4.6 30.2 1.0 CG A:GLU22 4.6 27.6 1.0 O A:HOH501 4.6 29.1 1.0 N A:LEU49 4.6 30.8 1.0 CB A:GLU22 4.7 27.1 1.0 CA A:LEU49 4.8 31.6 1.0 C4' C:DT15 5.0 33.7 1.0

Calcium binding site 6 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:41.9 occ:1.00 OP1 C:DA5 2.3 33.9 1.0 N A:SER243 3.0 31.6 1.0 OG A:SER243 3.2 32.8 1.0 CB A:SER243 3.3 31.0 1.0 P C:DA5 3.6 34.6 1.0 CA A:SER243 3.7 32.0 1.0 CG A:LYS241 3.8 32.9 1.0 N A:PHE242 3.8 32.6 1.0 OP2 C:DA5 4.0 33.7 1.0 C A:PHE242 4.1 31.7 1.0 CE A:LYS241 4.2 34.7 1.0 CB A:PHE242 4.2 32.3 1.0 CA A:PHE242 4.2 32.4 1.0 O3' C:DG4 4.5 34.9 1.0 C A:LYS241 4.5 32.8 1.0 CD A:LYS241 4.6 33.1 1.0 O5' C:DA5 4.7 34.3 1.0 CB A:LYS241 5.0 33.6 1.0 CA A:LYS241 5.0 33.2 1.0

Calcium binding site 7 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:49.0 occ:1.00 OD1 A:ASP92 2.3 33.7 1.0 CG A:ASP92 3.6 31.4 1.0 OD2 A:ASP92 4.3 31.5 1.0 CB A:ASP92 4.5 29.9 1.0 CA A:ASP92 5.0 29.0 1.0

Calcium binding site 8 out of 8 in the Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Engineered Variant of I-Onui Meganuclease with Improved Stability and Fully Altered Specificity Targeting Human Chromosome 11 Trans Integration Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:37.3 occ:1.00 OP2 B:DC5 2.2 29.9 1.0 O A:HOH504 3.0 30.8 1.0 N A:ARG83 3.2 29.7 1.0 N A:THR82 3.2 28.2 1.0 O A:HOH507 3.3 27.4 1.0 P B:DC5 3.4 29.0 1.0 CB A:ARG83 3.7 29.8 1.0 O A:LYS80 3.8 28.8 1.0 CA A:VAL81 3.8 28.3 1.0 OP1 B:DC5 3.9 30.9 1.0 C A:VAL81 4.0 28.5 1.0 CA A:ARG83 4.0 29.6 1.0 C A:THR82 4.1 28.6 1.0 CA A:THR82 4.1 28.8 1.0 O5' B:DC5 4.2 30.4 1.0 CG1 A:VAL68 4.2 29.3 1.0 OG1 A:THR82 4.2 28.3 1.0 CG2 A:VAL68 4.3 29.8 1.0 C A:LYS80 4.5 28.3 1.0 CA A:GLY67 4.5 29.0 1.0 N A:VAL81 4.5 27.6 1.0 N A:VAL68 4.6 28.8 1.0 OD2 A:ASP86 4.7 29.7 1.0 O3' B:DT4 4.7 30.5 1.0 CB A:THR82 4.7 28.2 1.0 C A:GLY67 4.8 29.6 1.0 CB A:VAL68 4.8 30.4 1.0 C3' B:DT4 4.9 29.6 1.0 N A:GLY67 4.9 29.0 1.0 CG1 A:VAL81 4.9 27.7 1.0 CB A:VAL81 4.9 27.4 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.