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Calcium in PDB 1bp7: Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna

Protein crystallography data

The structure of Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna, PDB code: 1bp7 was solved by M.S.Jurica, R.J.Monnat Junior, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.556, 89.259, 177.516, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 28.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna (pdb code 1bp7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna, PDB code: 1bp7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1bp7

Go back to Calcium Binding Sites List in 1bp7
Calcium binding site 1 out of 4 in the Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca202

b:9.7
occ:1.00
 OD1 B:ASP20 2.5 8.7 1.0
O A:GLY19 2.5 24.2 1.0
OP1 2:DC14 2.6 10.5 1.0
OD2 B:ASP20 2.7 8.7 1.0
OP2 1:DG15 2.8 10.5 1.0
OP1 1:DG15 2.9 10.5 1.0
CG B:ASP20 2.9 8.7 1.0
P 1:DG15 3.0 10.5 1.0
O5' 1:DG15 3.2 10.5 1.0
C A:GLY19 3.6 3.4 1.0
P 2:DC14 3.7 10.5 1.0
O5' 2:DC14 3.9 10.5 1.0
NE2 B:GLN47 4.0 11.6 1.0
O3' 2:DA13 4.0 10.5 1.0
OD1 A:ASP20 4.1 2.2 1.0
CB B:ASP20 4.4 8.7 1.0
CA A:GLY19 4.4 3.4 1.0
O 1:HOH203 4.4 10.3 1.0
N A:ASP20 4.5 12.2 1.0
O3' 2:DC14 4.5 10.5 1.0
C5' 1:DG15 4.6 10.5 1.0
CA A:ASP20 4.6 12.2 1.0
C4' 2:DC14 4.6 10.5 1.0
O3' 1:DA14 4.6 10.5 1.0
O A:ASP18 4.7 2.0 1.0
C5' 2:DC14 4.9 10.5 1.0
C3' 2:DC14 5.0 10.5 1.0

Calcium binding site 2 out of 4 in 1bp7

Go back to Calcium Binding Sites List in 1bp7
Calcium binding site 2 out of 4 in the Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca204

b:9.7
occ:1.00
 OD2 D:ASP20 2.3 2.0 1.0
OP2 4:DG15 2.6 10.5 1.0
OP1 3:DA14 2.6 10.5 1.0
OD1 D:ASP20 2.6 2.0 1.0
O C:GLY19 2.6 23.6 1.0
CG D:ASP20 2.8 2.0 1.0
O C:HOH204 3.0 10.3 1.0
O5' 3:DA14 3.4 10.5 1.0
P 3:DA14 3.5 10.5 1.0
C C:GLY19 3.7 7.3 1.0
O3' 3:DG13 3.9 10.5 1.0
O C:HOH205 3.9 10.3 1.0
P 4:DG15 3.9 10.5 1.0
OP2 3:DG15 4.0 10.5 1.0
CB D:ASP20 4.2 2.0 1.0
CA C:GLY19 4.2 7.3 1.0
O C:ASP18 4.3 2.0 1.0
OE1 D:GLN47 4.3 23.1 1.0
OP1 4:DG15 4.5 10.5 1.0
C5' 3:DA14 4.7 10.5 1.0
OD1 C:ASP20 4.7 12.3 1.0
N C:ASP20 4.8 13.6 1.0
CD D:GLN47 4.8 23.1 1.0
C5' 4:DG15 4.8 10.5 1.0
O5' 4:DG15 4.8 10.5 1.0
OP2 3:DA14 4.9 10.5 1.0
C4' 3:DA14 4.9 10.5 1.0
O3' 4:DC14 5.0 10.5 1.0

Calcium binding site 3 out of 4 in 1bp7

Go back to Calcium Binding Sites List in 1bp7
Calcium binding site 3 out of 4 in the Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:9.7
occ:1.00
 O B:GLY19 2.6 18.7 1.0
OP2 2:DG15 2.7 10.5 1.0
OP1 1:DA14 2.7 10.5 1.0
OD2 A:ASP20 2.7 2.2 1.0
O B:HOH155 2.9 10.3 1.0
O 1:HOH203 3.1 10.3 1.0
OD1 A:ASP20 3.3 2.2 1.0
CG A:ASP20 3.4 2.2 1.0
P 1:DA14 3.6 10.5 1.0
O5' 1:DA14 3.7 10.5 1.0
P 2:DG15 3.7 10.5 1.0
OP1 2:DG15 3.7 10.5 1.0
C B:GLY19 3.7 12.8 1.0
O3' 1:DG13 3.8 10.5 1.0
O B:ASP18 4.1 2.0 1.0
OE1 A:GLN47 4.3 22.7 1.0
CA B:GLY19 4.4 12.8 1.0
C5' 2:DG15 4.6 10.5 1.0
O5' 2:DG15 4.6 10.5 1.0
N B:ASP20 4.8 10.9 1.0
CD A:GLN47 4.8 22.7 1.0
OP2 1:DG15 4.9 10.5 1.0
CB A:ASP20 4.9 2.2 1.0
O3' 2:DC14 4.9 10.5 1.0
C5' 1:DA14 5.0 10.5 1.0
CA B:ASP20 5.0 10.9 1.0
NE2 A:GLN47 5.0 22.7 1.0
OD1 B:ASP20 5.0 8.7 1.0

Calcium binding site 4 out of 4 in 1bp7

Go back to Calcium Binding Sites List in 1bp7
Calcium binding site 4 out of 4 in the Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Group I Mobile Intron Endonuclease I-Crei Complexed with Homing Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:9.7
occ:1.00
 O D:GLY19 2.4 13.9 1.0
OP1 4:DC14 2.6 10.5 1.0
OD2 C:ASP20 2.6 12.3 1.0
OD1 C:ASP20 2.7 12.3 1.0
CG C:ASP20 3.0 12.3 1.0
O C:HOH205 3.3 10.3 1.0
NE2 C:GLN47 3.5 22.3 1.0
O5' 3:DG15 3.5 10.5 1.0
C D:GLY19 3.5 17.9 1.0
OP1 3:DG15 3.6 10.5 1.0
P 4:DC14 3.7 10.5 1.0
P 3:DG15 3.8 10.5 1.0
O5' 4:DC14 3.9 10.5 1.0
O3' 4:DA13 4.0 10.5 1.0
OP2 3:DG15 4.0 10.5 1.0
O D:ASP18 4.1 2.0 1.0
CA D:GLY19 4.2 17.9 1.0
CB C:ASP20 4.4 12.3 1.0
N D:ASP20 4.6 2.4 1.0
CD C:GLN47 4.6 22.3 1.0
OD1 D:ASP20 4.6 2.0 1.0
C5' 3:DG15 4.8 10.5 1.0
CA D:ASP20 4.8 2.4 1.0
OE1 C:GLN47 4.9 22.3 1.0

Reference:

M.S.Jurica, R.J.Monnat Jr., B.L.Stoddard. Dna Recognition and Cleavage By the Laglidadg Homing Endonuclease I-Crei. Mol.Cell V. 2 469 1998.
ISSN: ISSN 1097-2765
PubMed: 9809068
DOI: 10.1016/S1097-2765(00)80146-X
Page generated: Thu Jul 11 06:30:35 2024

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