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Calcium in PDB 6uvw: Engineered Variant of I-Onui Meganuclease with Improved Thermostability

Protein crystallography data

The structure of Engineered Variant of I-Onui Meganuclease with Improved Thermostability, PDB code: 6uvw 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) 46.31 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.426, 82.259, 167.398, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability (pdb code 6uvw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability, PDB code: 6uvw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6uvw

Go back to Calcium Binding Sites List in 6uvw
Calcium binding site 1 out of 5 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:47.2
occ:1.00
 OP2 C:DA16 2.2 49.8 1.0
OP1 B:DC14 2.3 45.4 1.0
OE1 A:GLU178 2.4 48.2 1.0
O A:ALA21 2.4 49.0 1.0
O A:HOH504 2.5 41.2 1.0
P C:DA16 3.3 51.4 1.0
O A:HOH506 3.3 41.3 1.0
C A:ALA21 3.5 49.8 1.0
CD A:GLU178 3.5 49.2 1.0
P B:DC14 3.7 44.3 1.0
OP1 C:DA16 3.7 45.6 1.0
C5' C:DA16 3.7 47.8 1.0
O5' C:DA16 3.8 48.7 1.0
CA A:CA403 3.9 45.0 0.7
CA A:ALA21 4.0 47.0 1.0
OE2 A:GLU178 4.0 47.6 1.0
O3' B:DT13 4.1 46.4 1.0
O A:ASP20 4.3 49.3 1.0
OE1 A:GLN204 4.4 46.4 1.0
NE2 A:GLN204 4.4 42.3 1.0
N A:GLU22 4.6 46.1 1.0
OP2 B:DC14 4.6 45.6 1.0
C4' C:DA16 4.6 45.9 1.0
O3' C:DT15 4.6 51.0 1.0
C5' B:DC14 4.7 45.9 1.0
OE2 A:GLU22 4.7 49.2 1.0
C4' B:DC14 4.7 46.9 1.0
O5' B:DC14 4.7 48.0 1.0
CG A:GLU178 4.7 46.5 1.0
CD A:GLN204 4.7 43.9 1.0
CB A:ALA21 4.9 45.2 1.0
CA A:GLU22 5.0 47.3 1.0

Calcium binding site 2 out of 5 in 6uvw

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Calcium binding site 2 out of 5 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:51.1
occ:1.00
 OP2 B:DA15 2.3 47.3 1.0
OE1 A:GLU22 2.4 48.7 1.0
OP1 C:DT15 2.4 49.5 1.0
O A:HOH505 2.4 44.7 1.0
O A:GLY177 2.4 48.2 1.0
C A:GLY177 3.3 48.6 1.0
CD A:GLU22 3.5 49.4 1.0
CA A:GLY177 3.6 46.1 1.0
P B:DA15 3.6 48.8 1.0
P C:DT15 3.8 47.7 1.0
CA A:CA403 4.0 45.0 0.7
C5' B:DA15 4.0 49.2 1.0
OE2 A:GLU22 4.0 49.2 1.0
O5' B:DA15 4.1 48.3 1.0
O A:SER176 4.3 48.5 1.0
O3' C:DA14 4.3 53.4 1.0
OP1 B:DA15 4.4 48.6 1.0
C5' C:DT15 4.5 52.5 1.0
N A:GLU178 4.5 45.9 1.0
CE A:LYS262 4.6 51.4 1.0
OE2 A:GLU178 4.7 47.6 1.0
C4' C:DT15 4.7 51.6 1.0
O5' C:DT15 4.7 49.6 1.0
CG A:GLU22 4.7 47.6 1.0
N A:GLY177 4.7 47.1 1.0
OP2 C:DT15 4.8 54.9 1.0
O3' B:DC14 4.8 46.9 1.0
C A:SER176 5.0 49.1 1.0
C4' B:DA15 5.0 48.5 1.0

Calcium binding site 3 out of 5 in 6uvw

Go back to Calcium Binding Sites List in 6uvw
Calcium binding site 3 out of 5 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:45.0
occ:0.69
 OE2 A:GLU178 2.2 47.6 1.0
OP2 C:DA16 2.2 49.8 1.0
OE2 A:GLU22 2.3 49.2 1.0
OP2 B:DA15 2.6 47.3 1.0
O3' C:DT15 2.8 51.0 1.0
O3' B:DC14 2.9 46.9 1.0
CD A:GLU178 3.0 49.2 1.0
P C:DA16 3.1 51.4 1.0
CD A:GLU22 3.1 49.4 1.0
OE1 A:GLU178 3.1 48.2 1.0
OE1 A:GLU22 3.2 48.7 1.0
P B:DA15 3.3 48.8 1.0
C3' C:DT15 3.7 50.0 1.0
C3' B:DC14 3.8 49.0 1.0
CA A:CA401 3.9 47.2 1.0
CA A:CA402 4.0 51.1 1.0
O5' C:DA16 4.0 48.7 1.0
O A:GLY177 4.0 48.2 1.0
C4' B:DC14 4.1 46.9 1.0
C4' C:DT15 4.1 51.6 1.0
O5' B:DA15 4.1 48.3 1.0
O A:ALA21 4.1 49.0 1.0
OP1 C:DA16 4.2 45.6 1.0
C A:GLY177 4.3 48.6 1.0
C A:ALA21 4.3 49.8 1.0
CG A:GLU178 4.3 46.5 1.0
CG A:GLU22 4.5 47.6 1.0
OP1 B:DA15 4.5 48.6 1.0
N A:GLU22 4.7 46.1 1.0
CB A:ALA21 4.7 45.2 1.0
N A:GLU178 4.7 45.9 1.0
OP1 B:DC14 4.7 45.4 1.0
CA A:GLU178 4.8 45.2 1.0
C5' C:DT15 4.8 52.5 1.0
C5' B:DC14 4.8 45.9 1.0
CA A:GLU22 4.8 47.3 1.0
CA A:ALA21 4.9 47.0 1.0
CA A:GLY177 4.9 46.1 1.0
CB A:GLU178 5.0 46.3 1.0

Calcium binding site 4 out of 5 in 6uvw

Go back to Calcium Binding Sites List in 6uvw
Calcium binding site 4 out of 5 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:44.5
occ:1.00
 OE1 D:GLU178 2.3 45.7 1.0
OP1 E:DC14 2.3 45.1 1.0
OP2 F:DA16 2.3 47.7 1.0
O D:ALA21 2.5 44.7 1.0
O D:HOH503 2.5 46.5 1.0
O E:HOH101 2.6 47.5 1.0
CD D:GLU178 3.3 48.0 1.0
C D:ALA21 3.4 45.2 1.0
P F:DA16 3.4 50.4 1.0
O D:HOH501 3.7 39.8 1.0
P E:DC14 3.7 43.3 1.0
OE2 D:GLU178 3.7 51.8 1.0
CA D:ALA21 3.8 45.8 1.0
C5' F:DA16 3.9 50.9 1.0
OP1 F:DA16 3.9 47.8 1.0
O5' F:DA16 4.0 48.4 1.0
O3' E:DT13 4.1 50.5 1.0
OE1 D:GLN204 4.2 46.5 1.0
O D:ASP20 4.3 45.4 1.0
NE2 D:GLN204 4.3 42.5 1.0
N D:GLU22 4.5 44.8 1.0
OE1 D:GLU22 4.5 47.0 1.0
C5' E:DC14 4.5 47.1 1.0
C4' E:DC14 4.6 48.4 1.0
CB D:ALA21 4.6 47.5 1.0
CG D:GLU178 4.6 47.0 1.0
OP2 E:DC14 4.6 47.6 1.0
CD D:GLN204 4.7 47.1 1.0
O5' E:DC14 4.7 48.3 1.0
O3' F:DT15 4.7 54.4 1.0
C4' F:DA16 4.8 50.7 1.0
N D:ALA21 4.9 46.0 1.0
CA D:GLU22 5.0 48.3 1.0

Calcium binding site 5 out of 5 in 6uvw

Go back to Calcium Binding Sites List in 6uvw
Calcium binding site 5 out of 5 in the Engineered Variant of I-Onui Meganuclease with Improved Thermostability


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 Thermostability within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:50.8
occ:1.00
 OE2 D:GLU22 2.2 45.8 1.0
OP2 E:DA15 2.3 49.2 1.0
OP1 F:DT15 2.4 50.9 1.0
O D:GLY177 2.5 51.8 1.0
O D:HOH504 2.5 49.9 1.0
O D:HOH509 2.7 52.7 0.9
CD D:GLU22 3.4 48.1 1.0
C D:GLY177 3.4 49.6 1.0
P E:DA15 3.5 50.0 1.0
CA D:GLY177 3.7 47.0 1.0
P F:DT15 3.8 50.0 1.0
OE1 D:GLU22 3.9 47.0 1.0
O D:HOH501 4.0 39.8 1.0
OP1 E:DA15 4.1 51.8 1.0
C5' E:DA15 4.1 50.4 1.0
O5' E:DA15 4.1 50.1 1.0
O3' F:DA14 4.2 48.6 1.0
C5' F:DT15 4.5 51.5 1.0
CG D:GLU22 4.5 48.5 1.0
N D:GLU178 4.5 48.4 1.0
O D:SER176 4.6 55.9 1.0
C4' F:DT15 4.6 49.8 1.0
O5' F:DT15 4.7 53.9 1.0
O3' E:DC14 4.7 48.5 1.0
OP2 F:DT15 4.8 52.0 1.0
CE D:LYS262 4.8 50.3 1.0
OE2 D:GLU178 4.9 51.8 1.0
N D:GLY177 4.9 50.2 1.0
C4' E:DA15 4.9 49.9 1.0

Reference:

R.Werther, B.L.Stoddard. Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein Dna-Binding Specificity To Be Published.
Page generated: Tue Jul 16 16:02:31 2024

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