Calcium in PDB 5t2n: Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui

Protein crystallography data

The structure of Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui, PDB code: 5t2n was solved by B.L.Stoddard, R.Werther, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.91 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.834, 67.421, 166.883, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui (pdb code 5t2n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui, PDB code: 5t2n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5t2n

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Calcium binding site 1 out of 4 in the Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 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 Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:40.9
occ:1.00
OE2 A:GLU22 2.3 44.7 1.0
OP2 B:DT15 2.4 39.3 1.0
OP1 C:DA15 2.4 35.1 1.0
O A:HOH533 2.4 43.2 1.0
O A:GLY177 2.4 38.9 1.0
O A:HOH507 2.5 37.5 1.0
C A:GLY177 3.4 41.1 1.0
CD A:GLU22 3.5 42.6 1.0
CA A:CA403 3.7 40.1 0.6
O B:HOH102 3.7 38.0 1.0
P B:DT15 3.7 41.7 1.0
CA A:GLY177 3.8 35.1 1.0
P C:DA15 3.8 38.1 1.0
OE1 A:GLU22 3.9 50.8 1.0
O5' B:DT15 4.3 39.7 1.0
O3' C:DA14 4.3 43.0 1.0
C5' B:DT15 4.3 40.5 1.0
O A:SER176 4.4 43.9 1.0
OP1 B:DT15 4.5 41.8 1.0
C5' C:DA15 4.5 40.9 1.0
N A:GLU178 4.6 37.1 1.0
C4' C:DA15 4.6 40.7 1.0
CE A:LYS262 4.6 42.4 1.0
O A:HOH532 4.7 42.8 1.0
CG A:GLU22 4.7 40.1 1.0
O5' C:DA15 4.7 39.6 1.0
OP2 C:DA15 4.8 39.4 1.0
OE1 A:GLU178 4.8 43.3 1.0
O3' B:DC14 4.8 40.5 1.0
N A:GLY177 4.9 37.8 1.0

Calcium binding site 2 out of 4 in 5t2n

Go back to Calcium Binding Sites List in 5t2n
Calcium binding site 2 out of 4 in the Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 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 Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:39.9
occ:1.00
OE2 A:GLU178 2.3 40.4 1.0
OP1 B:DC14 2.3 38.4 1.0
OP2 C:DG16 2.3 40.6 1.0
O A:ALA21 2.4 40.1 1.0
O A:HOH508 2.4 39.4 1.0
O B:HOH107 2.5 42.4 1.0
CD A:GLU178 3.3 38.6 1.0
C A:ALA21 3.4 36.3 1.0
P C:DG16 3.6 42.5 1.0
OE1 A:GLU178 3.6 43.3 1.0
P B:DC14 3.7 41.9 1.0
CA A:ALA21 3.9 36.7 1.0
C5' C:DG16 3.9 48.0 1.0
O A:HOH516 3.9 54.4 1.0
CA A:CA403 4.0 40.1 0.6
O5' C:DG16 4.0 44.9 1.0
O3' B:DT13 4.2 38.5 1.0
OE1 A:GLN204 4.2 39.3 1.0
O A:ASP20 4.2 37.5 1.0
OP1 C:DG16 4.2 44.4 1.0
NE2 A:GLN204 4.2 37.6 1.0
N A:GLU22 4.6 38.6 1.0
OP2 B:DC14 4.6 44.2 1.0
OE1 A:GLU22 4.6 50.8 1.0
C4' B:DC14 4.6 39.9 1.0
CD A:GLN204 4.6 45.3 1.0
C5' B:DC14 4.7 40.1 1.0
CG A:GLU178 4.7 39.8 1.0
O5' B:DC14 4.7 42.5 1.0
O3' C:DA15 4.8 43.8 1.0
CB A:ALA21 4.8 38.9 1.0
C4' C:DG16 4.9 44.6 1.0
N A:ALA21 4.9 32.0 1.0

Calcium binding site 3 out of 4 in 5t2n

Go back to Calcium Binding Sites List in 5t2n
Calcium binding site 3 out of 4 in the Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 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 Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:40.1
occ:0.58
OE1 A:GLU178 2.3 43.3 1.0
OE1 A:GLU22 2.4 50.8 1.0
OP2 B:DT15 2.4 39.3 1.0
OP2 C:DG16 2.5 40.6 1.0
O3' B:DC14 2.8 40.5 1.0
O3' C:DA15 2.9 43.8 1.0
CD A:GLU22 3.1 42.6 1.0
OE2 A:GLU22 3.2 44.7 1.0
P B:DT15 3.2 41.7 1.0
P C:DG16 3.3 42.5 1.0
CD A:GLU178 3.4 38.6 1.0
CA A:CA401 3.7 40.9 1.0
C3' C:DA15 3.7 40.7 1.0
C3' B:DC14 3.8 41.9 1.0
OE2 A:GLU178 3.8 40.4 1.0
O A:GLY177 3.9 38.9 1.0
CA A:CA402 4.0 39.9 1.0
C4' C:DA15 4.0 40.7 1.0
O A:ALA21 4.0 40.1 1.0
O5' B:DT15 4.2 39.7 1.0
C4' B:DC14 4.2 39.9 1.0
O5' C:DG16 4.2 44.9 1.0
C A:GLY177 4.3 41.1 1.0
OP1 B:DT15 4.3 41.8 1.0
OP1 C:DG16 4.4 44.4 1.0
CG A:GLU22 4.5 40.1 1.0
C A:ALA21 4.6 36.3 1.0
CG A:GLU178 4.6 39.8 1.0
OP1 C:DA15 4.7 35.1 1.0
CA A:GLU178 4.8 37.2 1.0
C5' C:DA15 4.8 40.9 1.0
N A:GLU178 4.8 37.1 1.0
OP1 B:DC14 4.9 38.4 1.0
CA A:GLY177 5.0 35.1 1.0

Calcium binding site 4 out of 4 in 5t2n

Go back to Calcium Binding Sites List in 5t2n
Calcium binding site 4 out of 4 in the Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 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 4 of Engineered Variant of I-Onui Meganuclease Targeting the Anopheles AGAP007280 Gene; Harbors 38 Point Mutations Relative to Wild-Type I- Onui within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:78.3
occ:1.00
O A:HOH531 2.4 64.5 1.0
NZ A:LYS299 3.4 65.5 1.0
N3 C:DA11 3.8 55.1 1.0
O2 B:DT16 4.4 51.3 1.0
C5' C:DG12 4.5 67.3 1.0
O4' C:DG12 4.5 54.5 1.0
C1' C:DA11 4.5 62.4 1.0
C2 C:DA11 4.5 52.5 1.0
O4' C:DA11 4.6 64.7 1.0
CE A:LYS299 4.6 74.4 1.0
C4' C:DG12 4.7 61.0 1.0
C4' B:DC17 4.7 54.8 1.0
O4' B:DC17 4.8 56.2 1.0
C4 C:DA11 4.9 55.6 1.0
CD A:LYS299 4.9 74.2 1.0
C5' B:DC17 4.9 52.7 1.0

Reference:

B.L.Stoddard, R.Werther. Tbd To Be Published.
Page generated: Sat Dec 12 05:43:16 2020

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