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Calcium in PDB 7rcc: First Stage Engineered Variant of I-Onui After Initial Reassembly

Protein crystallography data

The structure of First Stage Engineered Variant of I-Onui After Initial Reassembly, PDB code: 7rcc was solved by N.C.Ubilla-Rodriguez, R.A.Werther, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.841, 119.741, 165.101, 90, 90, 90
R / Rfree (%) 22.2 / 27.2

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the First Stage Engineered Variant of I-Onui After Initial Reassembly (pdb code 7rcc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the First Stage Engineered Variant of I-Onui After Initial Reassembly, PDB code: 7rcc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 7rcc

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Calcium binding site 1 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:47.1
occ:1.00
OD2 A:ASP178 2.2 29.8 1.0
OP2 F:DC16 2.3 27.9 1.0
OP2 E:DC15 2.5 26.6 1.0
OE1 A:GLU22 2.7 31.1 1.0
O3' E:DC14 2.8 27.1 1.0
OE2 A:GLU22 3.0 31.0 1.0
O3' F:DT15 3.0 25.3 1.0
CD A:GLU22 3.1 28.4 1.0
P E:DC15 3.2 24.8 1.0
P F:DC16 3.3 29.6 1.0
CA A:CA403 3.4 23.6 1.0
CG A:ASP178 3.5 29.1 1.0
C3' E:DC14 3.8 29.9 1.0
CA A:CA402 3.8 28.5 1.0
O A:GLY177 3.8 24.6 1.0
O A:ALA21 3.9 35.1 1.0
C3' F:DT15 3.9 25.0 1.0
C4' E:DC14 4.1 31.0 1.0
O5' E:DC15 4.1 26.9 1.0
O5' F:DC16 4.2 25.3 1.0
OD1 A:ASP178 4.2 26.7 1.0
C A:GLY177 4.2 27.9 1.0
C4' F:DT15 4.2 28.2 1.0
CA A:ASP178 4.3 27.0 1.0
CG A:GLU22 4.4 23.7 1.0
OP1 F:DC16 4.4 28.3 1.0
OP1 E:DC15 4.4 26.7 1.0
CB A:ASP178 4.5 28.5 1.0
N A:ASP178 4.5 26.9 1.0
OP1 E:DC14 4.5 35.6 1.0
C A:ALA21 4.6 30.2 1.0
C5' F:DT15 4.8 26.6 1.0
OP1 F:DT15 4.9 31.3 1.0
O F:HOH103 4.9 28.9 1.0
CB A:ALA21 5.0 28.9 1.0

Calcium binding site 2 out of 11 in 7rcc

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Calcium binding site 2 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:28.5
occ:1.00
OE2 A:GLU22 2.1 31.0 1.0
OP2 E:DC15 2.3 26.6 1.0
O A:GLY177 2.3 24.6 1.0
OP1 F:DT15 2.3 31.3 1.0
C A:GLY177 3.3 27.9 1.0
CD A:GLU22 3.3 28.4 1.0
P E:DC15 3.6 24.8 1.0
CA A:CA401 3.8 47.1 1.0
P F:DT15 3.8 26.8 1.0
CA A:GLY177 3.8 21.4 1.0
OE1 A:GLU22 3.9 31.1 1.0
O5' E:DC15 4.1 26.9 1.0
C5' E:DC15 4.2 26.7 1.0
C5' F:DT15 4.3 26.6 1.0
OP1 E:DC15 4.3 26.7 1.0
O A:SER176 4.4 31.0 1.0
O3' F:DA14 4.4 28.7 1.0
N A:ASP178 4.5 26.9 1.0
CG A:GLU22 4.5 23.7 1.0
O5' F:DT15 4.6 28.5 1.0
OP2 F:DT15 4.7 36.1 1.0
O3' E:DC14 4.8 27.1 1.0
C4' F:DT15 4.8 28.2 1.0
OD2 A:ASP178 4.8 29.8 1.0
CA A:ASP178 4.9 27.0 1.0
NZ A:LYS262 4.9 26.6 1.0
N A:GLY177 4.9 27.7 1.0

Calcium binding site 3 out of 11 in 7rcc

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Calcium binding site 3 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:23.6
occ:1.00
OP1 E:DC14 2.3 35.6 1.0
CA A:CA404 2.3 54.7 1.0
OP2 F:DC16 2.4 27.9 1.0
O F:HOH103 2.4 28.9 1.0
O A:ALA21 2.4 35.1 1.0
OD1 A:ASP178 2.5 26.7 1.0
OD2 A:ASP178 2.7 29.8 1.0
CG A:ASP178 3.0 29.1 1.0
C A:ALA21 3.4 30.2 1.0
CA A:CA401 3.4 47.1 1.0
P E:DC14 3.7 28.4 1.0
P F:DC16 3.7 29.6 1.0
CA A:ALA21 3.7 27.6 1.0
O3' E:DC13 4.1 33.8 1.0
OE1 A:GLN204 4.1 30.2 1.0
OP1 F:DC16 4.3 28.3 1.0
CB A:ALA21 4.3 28.9 1.0
O5' F:DC16 4.3 25.3 1.0
C4' E:DC14 4.4 31.0 1.0
NE2 A:GLN204 4.4 26.9 1.0
C5' F:DC16 4.4 28.4 1.0
CB A:ASP178 4.4 28.5 1.0
C5' E:DC14 4.6 27.8 1.0
OP2 E:DC14 4.6 32.5 1.0
N A:GLU22 4.6 24.9 1.0
O A:ASP20 4.7 20.8 1.0
CD A:GLN204 4.7 29.0 1.0
O5' E:DC14 4.7 35.0 1.0
OE1 A:GLU22 4.7 31.1 1.0
O3' F:DT15 4.8 25.3 1.0
N A:ALA21 5.0 26.7 1.0

Calcium binding site 4 out of 11 in 7rcc

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Calcium binding site 4 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:54.7
occ:1.00
CA A:CA403 2.3 23.6 1.0
O A:ASP20 2.9 20.8 1.0
O F:HOH103 2.9 28.9 1.0
NE2 A:GLN204 3.0 26.9 1.0
O A:ALA21 3.1 35.1 1.0
OD1 A:ASP178 3.2 26.7 1.0
OP1 E:DC14 3.4 35.6 1.0
CA A:ALA21 3.4 27.6 1.0
C A:ALA21 3.6 30.2 1.0
CD A:GLN204 3.8 29.0 1.0
OE1 A:GLN204 3.8 30.2 1.0
C A:ASP20 3.9 25.2 1.0
N A:ALA21 4.1 26.7 1.0
CG A:ASP178 4.2 29.1 1.0
OP2 F:DC16 4.4 27.9 1.0
P E:DC14 4.5 28.4 1.0
CB A:ALA21 4.5 28.9 1.0
CE1 A:PHE174 4.6 22.3 1.0
OD2 A:ASP178 4.6 29.8 1.0
OP2 E:DC14 4.7 32.5 1.0
N A:GLU22 4.8 24.9 1.0
CE A:LYS103 4.9 27.4 1.0

Calcium binding site 5 out of 11 in 7rcc

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Calcium binding site 5 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:45.4
occ:1.00
OP2 C:DC16 2.3 26.4 1.0
OD2 D:ASP178 2.4 26.1 1.0
OP2 B:DC15 2.5 28.6 1.0
OE1 D:GLU22 2.6 30.4 1.0
O3' C:DT15 2.7 25.8 1.0
O3' B:DC14 3.0 27.1 1.0
P C:DC16 3.1 23.5 1.0
OE2 D:GLU22 3.1 32.7 1.0
CD D:GLU22 3.1 30.2 1.0
P B:DC15 3.3 28.6 1.0
C3' C:DT15 3.6 24.4 1.0
CA D:CA403 3.6 25.4 1.0
CG D:ASP178 3.7 27.9 1.0
CA D:CA402 3.7 27.8 1.0
O D:ALA21 3.8 28.4 1.0
O5' C:DC16 3.9 21.4 1.0
C4' C:DT15 3.9 25.4 1.0
C3' B:DC14 4.0 28.9 1.0
O D:GLY177 4.0 20.7 1.0
C4' B:DC14 4.2 29.0 1.0
O5' B:DC15 4.3 25.5 1.0
OP1 C:DC16 4.3 30.3 1.0
C D:GLY177 4.4 25.4 1.0
CG D:GLU22 4.4 28.6 1.0
OD1 D:ASP178 4.4 22.1 1.0
OP1 B:DC15 4.4 32.3 1.0
C5' C:DT15 4.5 28.6 1.0
C D:ALA21 4.5 29.3 1.0
CA D:ASP178 4.5 26.0 1.0
CB D:ASP178 4.7 23.9 1.0
N D:ASP178 4.7 27.7 1.0
OP1 B:DC14 4.7 33.8 1.0
OP1 C:DT15 4.7 24.9 1.0
O C:HOH101 4.9 26.4 1.0
CA D:GLU22 4.9 20.6 1.0

Calcium binding site 6 out of 11 in 7rcc

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Calcium binding site 6 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:27.8
occ:1.00
OE2 D:GLU22 2.2 32.7 1.0
O D:GLY177 2.3 20.7 1.0
OP2 B:DC15 2.3 28.6 1.0
OP1 C:DT15 2.3 24.9 1.0
C D:GLY177 3.3 25.4 1.0
CD D:GLU22 3.3 30.2 1.0
P B:DC15 3.6 28.6 1.0
CA D:CA401 3.7 45.4 1.0
P C:DT15 3.8 26.9 1.0
OE1 D:GLU22 3.8 30.4 1.0
CA D:GLY177 3.9 23.4 1.0
O5' B:DC15 4.1 25.5 1.0
C5' B:DC15 4.1 26.9 1.0
C5' C:DT15 4.3 28.6 1.0
O3' C:DA14 4.3 35.6 1.0
OP1 B:DC15 4.3 32.3 1.0
N D:ASP178 4.4 27.7 1.0
O D:SER176 4.4 31.2 1.0
NZ D:LYS262 4.5 26.3 1.0
CG D:GLU22 4.6 28.6 1.0
O5' C:DT15 4.6 26.1 1.0
C4' C:DT15 4.7 25.4 1.0
OP2 C:DT15 4.7 31.9 1.0
O3' B:DC14 4.8 27.1 1.0
OD2 D:ASP178 4.8 26.1 1.0
CA D:ASP178 4.8 26.0 1.0
N D:GLY177 5.0 24.0 1.0

Calcium binding site 7 out of 11 in 7rcc

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Calcium binding site 7 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:25.4
occ:1.00
OP1 B:DC14 2.2 33.8 1.0
OP2 C:DC16 2.3 26.4 1.0
O D:HOH502 2.4 22.6 1.0
O C:HOH101 2.4 26.4 1.0
O D:ALA21 2.5 28.4 1.0
OD1 D:ASP178 2.5 22.1 1.0
OD2 D:ASP178 2.8 26.1 1.0
CG D:ASP178 3.0 27.9 1.0
C D:ALA21 3.5 29.3 1.0
P B:DC14 3.6 23.9 1.0
CA D:CA401 3.6 45.4 1.0
P C:DC16 3.7 23.5 1.0
CA D:ALA21 3.7 23.9 1.0
OE1 D:GLN204 4.0 25.7 1.0
O3' B:DC13 4.1 26.7 1.0
NE2 D:GLN204 4.3 17.5 1.0
O5' C:DC16 4.3 21.4 1.0
OP1 C:DC16 4.4 30.3 1.0
CB D:ALA21 4.4 28.7 1.0
C4' B:DC14 4.4 29.0 1.0
C5' C:DC16 4.4 27.4 1.0
CB D:ASP178 4.4 23.9 1.0
OP2 B:DC14 4.4 28.6 1.0
CD D:GLN204 4.5 27.7 1.0
C5' B:DC14 4.5 27.8 1.0
O D:ASP20 4.6 20.2 1.0
O5' B:DC14 4.6 27.8 1.0
N D:GLU22 4.7 23.8 1.0
O3' C:DT15 4.8 25.8 1.0
OE1 D:GLU22 5.0 30.4 1.0
N D:ALA21 5.0 24.2 1.0

Calcium binding site 8 out of 11 in 7rcc

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Calcium binding site 8 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:45.9
occ:1.00
OP2 H:DC15 2.4 25.9 1.0
OP2 I:DC16 2.4 32.1 1.0
OD2 G:ASP178 2.5 24.0 1.0
OE1 G:GLU22 2.5 33.3 1.0
OE2 G:GLU22 2.9 26.0 1.0
CD G:GLU22 2.9 27.5 1.0
O3' I:DT15 2.9 30.4 1.0
O3' H:DC14 3.0 30.1 1.0
P I:DC16 3.2 33.1 1.0
P H:DC15 3.2 25.8 1.0
CA G:CA403 3.6 24.2 1.0
CA G:CA402 3.6 27.2 1.0
CG G:ASP178 3.7 26.1 1.0
C3' I:DT15 3.7 30.1 1.0
O G:ALA21 3.9 26.2 1.0
O G:GLY177 4.0 28.7 1.0
C3' H:DC14 4.0 27.4 1.0
O5' I:DC16 4.1 24.3 1.0
C4' I:DT15 4.1 31.4 1.0
O5' H:DC15 4.2 24.2 1.0
CG G:GLU22 4.2 23.6 1.0
C G:GLY177 4.2 30.9 1.0
C4' H:DC14 4.3 32.8 1.0
OP1 H:DC15 4.4 28.0 1.0
CA G:ASP178 4.4 29.7 1.0
OP1 I:DC16 4.4 30.3 1.0
C G:ALA21 4.5 30.4 1.0
OD1 G:ASP178 4.5 25.7 1.0
N G:ASP178 4.6 23.1 1.0
C5' I:DT15 4.6 29.2 1.0
CB G:ASP178 4.6 24.9 1.0
OP1 I:DT15 4.7 26.9 1.0
OP1 H:DC14 4.8 38.5 1.0
CA G:GLU22 4.9 23.2 1.0
CB G:GLU22 4.9 26.9 1.0
CA G:GLY177 5.0 26.6 1.0

Calcium binding site 9 out of 11 in 7rcc

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Calcium binding site 9 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca402

b:27.2
occ:1.00
OE2 G:GLU22 2.2 26.0 1.0
CA G:CA404 2.2 52.1 1.0
OP2 H:DC15 2.3 25.9 1.0
OP1 I:DT15 2.3 26.9 1.0
O G:GLY177 2.4 28.7 1.0
O G:HOH502 2.4 24.8 1.0
CD G:GLU22 3.3 27.5 1.0
C G:GLY177 3.4 30.9 1.0
P H:DC15 3.6 25.8 1.0
CA G:CA401 3.6 45.9 1.0
P I:DT15 3.8 26.7 1.0
OE1 G:GLU22 3.8 33.3 1.0
CA G:GLY177 3.8 26.6 1.0
O5' H:DC15 4.1 24.2 1.0
C5' H:DC15 4.2 26.9 1.0
OP1 H:DC15 4.3 28.0 1.0
O3' I:DA14 4.3 27.8 1.0
C5' I:DT15 4.4 29.2 1.0
O G:SER176 4.5 29.9 1.0
CG G:GLU22 4.5 23.6 1.0
N G:ASP178 4.5 23.1 1.0
O5' I:DT15 4.6 25.9 1.0
NZ G:LYS262 4.7 30.0 1.0
O3' H:DC14 4.7 30.1 1.0
C4' I:DT15 4.7 31.4 1.0
OP2 I:DT15 4.8 33.9 1.0
CA G:ASP178 4.9 29.7 1.0
OD2 G:ASP178 5.0 24.0 1.0
N G:GLY177 5.0 26.4 1.0

Calcium binding site 10 out of 11 in 7rcc

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Calcium binding site 10 out of 11 in the First Stage Engineered Variant of I-Onui After Initial Reassembly


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of First Stage Engineered Variant of I-Onui After Initial Reassembly within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca403

b:24.2
occ:1.00
OP2 I:DC16 2.2 32.1 1.0
OP1 H:DC14 2.2 38.5 1.0
O G:ALA21 2.4 26.2 1.0
O I:HOH102 2.6 24.7 1.0
OD2 G:ASP178 2.6 24.0 1.0
O G:HOH501 2.6 28.7 1.0
OD1 G:ASP178 2.7 25.7 1.0
CG G:ASP178 3.0 26.1 1.0
C G:ALA21 3.4 30.4 1.0
CA G:CA401 3.6 45.9 1.0
P I:DC16 3.6 33.1 1.0
P H:DC14 3.6 27.0 1.0
CA G:ALA21 3.7 25.7 1.0
O3' H:DC13 4.1 33.0 1.0
OE1 G:GLN204 4.2 27.0 1.0
O5' I:DC16 4.2 24.3 1.0
OP1 I:DC16 4.3 30.3 1.0
NE2 G:GLN204 4.3 20.0 1.0
C5' I:DC16 4.3 27.4 1.0
CB G:ALA21 4.3 25.7 1.0
C4' H:DC14 4.4 32.8 1.0
CB G:ASP178 4.5 24.9 1.0
OP2 H:DC14 4.5 34.0 1.0
C5' H:DC14 4.6 33.2 1.0
O G:ASP20 4.6 27.2 1.0
N G:GLU22 4.6 24.9 1.0
CD G:GLN204 4.6 29.8 1.0
O5' H:DC14 4.6 28.8 1.0
O3' I:DT15 4.7 30.4 1.0
OE1 G:GLU22 4.8 33.3 1.0
N G:ALA21 5.0 29.1 1.0
O3' H:DC14 5.0 30.1 1.0

Reference:

R.A.Werther, N.C.Ubilla-Rodriguez, A.T.Smiley, K.Havens, A.R.Lambert, B.L.Stoddard. Characterization of the Stepwise Engineering and Optimization of A Retargeted Dna Binding Protein and Gene-Editing Meganuclease To Be Published.
Page generated: Thu Jul 10 00:43:36 2025

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