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Calcium in PDB 6opm: Casposase Bound to Integration Product

Protein crystallography data

The structure of Casposase Bound to Integration Product, PDB code: 6opm was solved by F.Dyda, A.B.Hickman, S.Kailasan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 3.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.390, 106.390, 423.360, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Casposase Bound to Integration Product (pdb code 6opm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Casposase Bound to Integration Product, PDB code: 6opm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6opm

Go back to Calcium Binding Sites List in 6opm
Calcium binding site 1 out of 6 in the Casposase Bound to Integration Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Casposase Bound to Integration Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:0.1
occ:1.00
OD2 A:ASP46 3.0 0.4 1.0
CA A:MSE1 3.7 0.5 1.0
O A:ASP44 3.8 0.4 1.0
CG A:ASP46 4.0 0.1 1.0
OE1 D:GLN189 4.0 0.3 1.0
CB A:MSE1 4.1 0.7 1.0
CB A:ASP46 4.2 0.8 1.0
N A:MSE1 4.2 0.8 1.0
CG A:MSE1 4.3 0.3 1.0
N A:LYS2 4.5 0.1 1.0
OP2 F:DC21 4.6 0.7 1.0
N A:ASP46 4.7 0.9 1.0
CA A:ASP46 4.7 0.7 1.0
C A:MSE1 4.7 0.1 1.0
CA A:CA502 4.9 0.3 1.0
C A:ASP44 5.0 0.8 1.0

Calcium binding site 2 out of 6 in 6opm

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Calcium binding site 2 out of 6 in the Casposase Bound to Integration Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Casposase Bound to Integration Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:0.3
occ:1.00
OD2 A:ASP46 3.2 0.4 1.0
CG A:ASP46 3.5 0.1 1.0
OD1 A:ASP46 3.5 0.2 1.0
ND2 A:ASN69 3.7 0.3 1.0
NZ A:LYS217 3.9 0.1 1.0
OP2 F:DC21 4.0 0.7 1.0
O A:ASN69 4.2 0.5 1.0
CA A:ASP46 4.4 0.7 1.0
CB A:ASP46 4.5 0.8 1.0
CE A:LYS217 4.6 0.5 1.0
CD A:LYS217 4.7 0.1 1.0
O A:ASP46 4.7 0.6 1.0
CG A:ASN69 4.9 0.7 1.0
CA A:CA501 4.9 0.1 1.0

Calcium binding site 3 out of 6 in 6opm

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Calcium binding site 3 out of 6 in the Casposase Bound to Integration Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Casposase Bound to Integration Product within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:0.5
occ:1.00
OP2 E:DC21 2.8 0.4 1.0
OD1 C:ASP46 3.2 0.4 1.0
CE C:LYS217 3.5 0.6 1.0
O C:HOH604 3.7 1.0 1.0
P E:DC21 4.1 0.2 1.0
CG C:ASP46 4.3 0.8 1.0
CD C:LYS217 4.5 0.8 1.0
NZ C:LYS217 4.5 0.9 1.0
CB C:ASP46 4.6 0.7 1.0
O3' E:DG20 4.6 0.6 1.0
OP1 E:DC21 4.6 0.4 1.0
C3' E:DG20 4.6 0.1 1.0
CA C:CA502 4.7 0.5 1.0

Calcium binding site 4 out of 6 in 6opm

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Calcium binding site 4 out of 6 in the Casposase Bound to Integration Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Casposase Bound to Integration Product within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:0.5
occ:1.00
O C:HOH602 2.5 0.4 1.0
OD1 C:ASP46 2.5 0.4 1.0
OD2 C:ASP46 3.0 0.5 1.0
O C:HOH604 3.1 1.0 1.0
CG C:ASP46 3.1 0.8 1.0
CA C:MSE1 3.6 0.6 1.0
N C:MSE1 3.8 0.2 1.0
OP2 E:DC21 3.9 0.4 1.0
CB C:MSE1 4.0 0.9 1.0
CG C:MSE1 4.2 0.3 1.0
CB C:ASP46 4.6 0.7 1.0
O5' E:DC21 4.7 0.0 1.0
CA C:CA501 4.7 0.5 1.0
P E:DC21 4.7 0.2 1.0
C C:MSE1 4.8 0.6 1.0
N C:LYS2 4.8 0.9 1.0
O C:ASP44 4.9 0.7 1.0

Calcium binding site 5 out of 6 in 6opm

Go back to Calcium Binding Sites List in 6opm
Calcium binding site 5 out of 6 in the Casposase Bound to Integration Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Casposase Bound to Integration Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca101

b:0.4
occ:1.00
O2 E:DC7 2.6 0.9 1.0
OP1 E:DC7 2.6 0.3 1.0
O E:HOH203 2.8 78.4 1.0
O F:HOH201 2.8 0.6 1.0
C2 E:DC7 3.6 0.7 1.0
N3 E:DC7 4.0 0.6 1.0
P E:DC7 4.1 0.9 1.0
N4 E:DC8 4.1 0.8 1.0
C5' E:DC7 4.3 0.8 1.0
O5' E:DC7 4.6 0.6 1.0
C5 E:DC8 4.6 1.0 1.0
C4 E:DC8 4.7 0.1 1.0
C3' E:DC6 4.7 0.7 1.0
O3' E:DC6 4.8 0.5 1.0
O5' E:DC6 4.8 0.6 1.0
N1 E:DC7 4.9 0.0 1.0

Calcium binding site 6 out of 6 in 6opm

Go back to Calcium Binding Sites List in 6opm
Calcium binding site 6 out of 6 in the Casposase Bound to Integration Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Casposase Bound to Integration Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:98.8
occ:1.00
OP1 F:DC7 2.2 96.3 1.0
O F:HOH205 2.3 87.8 1.0
O2 F:DC7 2.5 98.5 1.0
O F:HOH204 2.8 65.8 1.0
O F:HOH206 2.9 92.0 1.0
O E:HOH202 3.2 92.6 1.0
C2 F:DC7 3.5 99.5 1.0
P F:DC7 3.6 94.0 1.0
N3 F:DC7 3.8 0.9 1.0
C5' F:DC7 4.1 96.7 1.0
O5' F:DC7 4.2 94.1 1.0
O3' F:DC6 4.4 95.9 1.0
C3' F:DC6 4.4 97.2 1.0
N4 F:DC8 4.5 0.8 1.0
N1 F:DC7 4.7 98.3 1.0
OP2 F:DC7 4.7 89.9 1.0
O4' F:DC7 4.8 97.1 1.0
O5' F:DC6 4.9 96.1 1.0
CE B:MSE194 4.9 0.2 1.0

Reference:

F.Dyda, A.B.Hickman, S.Kailasan. Casposase Bound to Integration Product To Be Published.
Page generated: Tue Jul 16 12:34:00 2024

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