Atomistry » Calcium » PDB 1bjq-1byh » 1bp7
Atomistry »
  Calcium »
    PDB 1bjq-1byh »
      1bp7 »

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: Mon Jul 7 13:46:15 2025

Last articles

Mg in 7EQD
Mg in 7EWA
Mg in 7EW9
Mg in 7EV7
Mg in 7EVI
Mg in 7EUQ
Mg in 7EUN
Mg in 7EV3
Mg in 7EV2
Mg in 7EUL
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy