Calcium in PDB 5t8d: Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui

Protein crystallography data

The structure of Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui, PDB code: 5t8d was solved by B.L.Stoddard, R.Werther, A.R.Lambert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.38 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.701, 75.007, 165.158, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui (pdb code 5t8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui, PDB code: 5t8d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5t8d

Go back to Calcium Binding Sites List in 5t8d
Calcium binding site 1 out of 3 in the Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui


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 Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:29.5
occ:1.00
OP1 C:DT15 2.3 29.2 1.0
OP2 B:DA17 2.3 28.7 1.0
O A:HOH566 2.3 31.2 1.0
OE2 A:GLU22 2.3 30.6 1.0
O A:GLY177 2.4 28.0 1.0
O A:HOH619 2.5 35.2 1.0
O C:HOH124 3.2 36.0 1.0
C A:GLY177 3.4 25.1 1.0
CD A:GLU22 3.5 30.6 1.0
P B:DA17 3.6 30.9 1.0
P C:DT15 3.7 30.3 1.0
CA A:GLY177 3.8 26.7 1.0
CA A:CA403 3.8 41.2 1.0
OE1 A:GLU22 4.0 32.7 1.0
O A:HOH544 4.2 29.0 1.0
O3' C:DA14 4.2 29.0 1.0
O5' B:DA17 4.2 28.0 1.0
C5' C:DT15 4.3 26.8 1.0
C5' B:DA17 4.3 25.1 1.0
OP1 B:DA17 4.4 27.8 1.0
C4' C:DT15 4.4 28.0 1.0
O A:SER176 4.5 25.9 1.0
O5' C:DT15 4.5 27.6 1.0
N A:GLU178 4.6 25.5 1.0
OP2 C:DT15 4.7 29.5 1.0
CG A:GLU22 4.7 28.5 1.0
O3' B:DC16 4.7 31.3 1.0
OE1 A:GLU178 4.9 31.9 1.0
N A:GLY177 4.9 28.9 1.0

Calcium binding site 2 out of 3 in 5t8d

Go back to Calcium Binding Sites List in 5t8d
Calcium binding site 2 out of 3 in the Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui


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 Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:27.0
occ:1.00
OP1 B:DC16 2.3 33.2 1.0
OP2 C:DA16 2.3 27.4 1.0
OE2 A:GLU178 2.3 28.7 1.0
O A:ALA21 2.3 28.8 1.0
O B:HOH145 2.5 30.6 1.0
O A:HOH540 2.5 26.6 1.0
CD A:GLU178 3.3 27.3 1.0
C A:ALA21 3.4 26.8 1.0
P C:DA16 3.5 28.4 1.0
OE1 A:GLU178 3.6 31.9 1.0
P B:DC16 3.7 32.7 1.0
CA A:CA403 3.8 41.2 1.0
CA A:ALA21 3.9 24.6 1.0
O5' C:DA16 4.0 28.0 1.0
C5' C:DA16 4.0 29.7 1.0
O A:HOH535 4.0 36.1 1.0
O3' B:DT15 4.1 32.5 1.0
OP1 C:DA16 4.2 32.6 1.0
OE1 A:GLN204 4.2 29.8 1.0
NE2 A:GLN204 4.3 27.3 1.0
OE1 A:GLU22 4.3 32.7 1.0
O A:ASP20 4.4 22.1 1.0
C5' B:DC16 4.5 29.4 1.0
N A:GLU22 4.6 23.9 1.0
C4' B:DC16 4.6 31.5 1.0
OP2 B:DC16 4.6 30.8 1.0
O5' B:DC16 4.6 28.8 1.0
CD A:GLN204 4.7 28.8 1.0
O3' C:DT15 4.7 31.3 1.0
CG A:GLU178 4.7 26.0 1.0
CB A:ALA21 4.7 23.6 1.0
C4' C:DA16 4.8 28.0 1.0
O B:HOH114 5.0 36.3 1.0
CA A:GLU22 5.0 25.2 1.0
N A:ALA21 5.0 24.8 1.0

Calcium binding site 3 out of 3 in 5t8d

Go back to Calcium Binding Sites List in 5t8d
Calcium binding site 3 out of 3 in the Engineered Variant of I-Onui Meganuclease Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui


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 Targeting the Hiv Integrase Gene; Harbors 47 Point Mutations Relative to Wild-Type I-Onui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:41.2
occ:1.00
OE1 A:GLU22 2.3 32.7 1.0
OE1 A:GLU178 2.3 31.9 1.0
OP2 C:DA16 2.4 27.4 1.0
OP2 B:DA17 2.5 28.7 1.0
O3' B:DC16 2.8 31.3 1.0
O3' C:DT15 2.9 31.3 1.0
CD A:GLU22 3.2 30.6 1.0
P B:DA17 3.2 30.9 1.0
P C:DA16 3.3 28.4 1.0
OE2 A:GLU22 3.3 30.6 1.0
CD A:GLU178 3.4 27.3 1.0
O A:GLY177 3.7 28.0 1.0
C3' B:DC16 3.7 29.2 1.0
OE2 A:GLU178 3.8 28.7 1.0
C3' C:DT15 3.8 28.8 1.0
CA A:CA402 3.8 27.0 1.0
CA A:CA401 3.8 29.5 1.0
O A:ALA21 4.0 28.8 1.0
C4' B:DC16 4.0 31.5 1.0
O5' B:DA17 4.1 28.0 1.0
C4' C:DT15 4.1 28.0 1.0
O5' C:DA16 4.2 28.0 1.0
C A:GLY177 4.2 25.1 1.0
OP1 B:DA17 4.4 27.8 1.0
OP1 C:DA16 4.5 32.6 1.0
CG A:GLU22 4.6 28.5 1.0
C A:ALA21 4.6 26.8 1.0
CG A:GLU178 4.6 26.0 1.0
CA A:GLU178 4.7 24.3 1.0
OP1 B:DC16 4.7 33.2 1.0
N A:GLU178 4.7 25.5 1.0
C5' B:DC16 4.8 29.4 1.0
C5' C:DT15 4.9 26.8 1.0
CA A:GLY177 4.9 26.7 1.0
CB A:ALA21 4.9 23.6 1.0
O B:HOH111 5.0 27.0 1.0

Reference:

B.L.Stoddard, B.L.Stoddard, R.Werther, A.R.Lambert. N/A N/A.
Page generated: Sat Dec 12 05:43:47 2020

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