Atomistry » Calcium » PDB 6ulb-6v4n » 6uvw
Atomistry »
  Calcium »
    PDB 6ulb-6v4n »
      6uvw »

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

Go back to Calcium Binding Sites List in 6uvw
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy