Calcium in PDB 1r7m: The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region

The structure of The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region, PDB code: 1r7m was solved by C.M.Moure, F.S.Gimble, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.35 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.600, 90.700, 115.300, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 26.7

The binding sites of Calcium atom in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region (pdb code 1r7m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region, PDB code: 1r7m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca305 b:26.0 occ:1.00 O D:HOH41 2.3 25.0 1.0 OP1 D:DT16 2.3 35.7 1.0 O D:HOH31 2.3 20.8 1.0 OP1 C:DC15 2.3 30.4 1.0 O C:HOH315 2.3 32.2 1.0 O D:HOH47 2.4 22.8 1.0 O4' D:DA15 3.7 30.9 1.0 P D:DT16 3.7 32.8 1.0 P C:DC15 3.7 26.8 1.0 C4' D:DA15 4.2 32.3 1.0 O3' C:DA14 4.2 28.5 1.0 O4' D:DT16 4.2 35.6 1.0 O4' C:DC15 4.3 25.6 1.0 O5' D:DT16 4.3 35.8 1.0 C4' D:DT16 4.4 32.4 1.0 N3 D:DA15 4.4 35.1 1.0 O D:HOH39 4.5 32.5 1.0 OP2 D:DT16 4.5 39.4 1.0 C1' D:DA15 4.6 33.7 1.0 O2 D:DT14 4.6 33.8 1.0 C4' C:DC15 4.6 26.7 1.0 O5' C:DC15 4.6 30.4 1.0 O C:HOH314 4.6 36.4 1.0 OP2 C:DC15 4.7 34.4 1.0 C5' D:DT16 4.7 33.4 1.0 N3 C:DA14 4.7 28.7 1.0 O3' D:DA15 4.8 36.1 1.0 O C:HOH324 4.8 31.4 1.0 C1' C:DA14 4.9 27.1 1.0 C2' C:DA14 5.0 27.6 1.0

Calcium binding site 2 out of 6 in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:32.8 occ:1.00 O F:HOH30 2.1 29.4 1.0 OP1 F:DT16 2.2 34.0 1.0 OP1 E:DC15 2.4 36.5 1.0 O E:HOH310 2.4 27.6 1.0 O E:HOH311 2.7 31.3 1.0 O F:HOH35 2.8 27.0 1.0 O4' F:DA15 3.5 34.7 1.0 P F:DT16 3.6 34.2 1.0 P E:DC15 3.8 34.9 1.0 C4' F:DA15 3.8 33.7 1.0 O4' E:DC15 4.2 29.6 1.0 OP2 F:DT16 4.3 37.6 1.0 O3' E:DA14 4.3 35.9 1.0 O5' F:DT16 4.3 38.6 1.0 C4' E:DC15 4.5 33.2 1.0 N3 F:DA15 4.5 34.5 1.0 C1' F:DA15 4.5 33.8 1.0 O4' F:DT16 4.6 31.1 1.0 OP2 E:DC15 4.7 37.4 1.0 O3' F:DA15 4.7 39.3 1.0 N3 E:DA14 4.8 31.3 1.0 O F:HOH31 4.8 38.6 1.0 C4' F:DT16 4.8 31.7 1.0 O5' E:DC15 4.8 37.0 1.0 O2 F:DT14 4.8 42.0 1.0 C3' F:DA15 4.8 35.1 1.0 C5' F:DA15 4.8 34.3 1.0 C5' F:DT16 4.9 33.7 1.0

Calcium binding site 3 out of 6 in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:30.8 occ:1.00 OD2 A:ASP44 2.3 24.1 1.0 O A:ASP144 2.4 29.7 1.0 O D:HOH30 2.4 34.1 1.0 OP1 C:DA14 2.4 28.6 1.0 OP1 D:DC17 2.5 38.4 1.0 CG A:ASP44 3.3 28.9 1.0 C A:ASP144 3.4 30.2 1.0 P D:DC17 3.6 35.0 1.0 OD1 A:ASP44 3.7 32.3 1.0 P C:DA14 3.9 28.4 1.0 OP2 D:DC17 3.9 40.2 1.0 CA A:ASP144 4.0 29.8 1.0 NZ A:LYS223 4.1 53.5 1.0 O3' C:DA13 4.4 31.4 1.0 O A:MET143 4.4 26.9 1.0 CD1 A:TRP62 4.5 24.1 1.0 C5' C:DA14 4.6 28.3 1.0 O5' D:DC17 4.6 37.9 1.0 N A:ASP145 4.6 30.3 1.0 C4' C:DA14 4.6 29.2 1.0 NE1 A:TRP62 4.6 26.9 1.0 C5' D:DC17 4.7 37.8 1.0 CB A:ASP44 4.7 27.9 1.0 C4' D:DC17 4.7 37.1 1.0 O5' C:DA14 4.8 30.7 1.0 O3' D:DT16 4.8 35.2 1.0 OP2 C:DA14 4.9 30.3 1.0 CB A:ASP144 4.9 31.0 1.0 CA A:ASP145 5.0 29.6 1.0

Calcium binding site 4 out of 6 in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:31.0 occ:1.00 O A:HOH327 2.2 35.6 1.0 OD1 A:ASP145 2.2 31.1 1.0 OP2 C:DC15 2.3 34.4 1.0 O A:GLY43 2.5 28.5 1.0 OD1 A:ASP44 2.5 32.3 1.0 OP2 D:DC17 2.5 40.2 1.0 CG A:ASP145 3.2 28.2 1.0 C A:GLY43 3.3 27.6 1.0 P C:DC15 3.7 26.8 1.0 O A:HOH311 3.7 37.3 1.0 CG A:ASP44 3.7 28.9 1.0 OD2 A:ASP145 3.8 26.9 1.0 P D:DC17 4.0 35.0 1.0 O A:HOH347 4.0 43.5 1.0 CA A:GLY43 4.1 27.2 1.0 O3' C:DA14 4.1 28.5 1.0 N A:ASP44 4.1 28.1 1.0 O D:HOH39 4.2 32.5 1.0 O A:ASN163 4.3 27.0 1.0 CB A:ASP145 4.3 28.3 1.0 CA A:ASP44 4.3 26.6 1.0 CA A:ASP145 4.4 29.6 1.0 OP1 C:DC15 4.5 30.4 1.0 OD2 A:ASP44 4.5 24.1 1.0 O3' D:DT16 4.6 35.2 1.0 O5' D:DT16 4.6 35.8 1.0 CB A:ASP44 4.6 27.9 1.0 N A:ASP145 4.7 30.3 1.0 OP1 D:DC17 4.8 38.4 1.0 O5' C:DC15 4.8 30.4 1.0 O A:ASP144 4.8 29.7 1.0 O5' D:DC17 4.8 37.9 1.0 C A:ASP144 4.9 30.2 1.0 C4' D:DT16 4.9 32.4 1.0 C3' D:DT16 4.9 34.0 1.0

Calcium binding site 5 out of 6 in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca536 b:29.7 occ:1.00 OP1 F:DC17 2.2 34.8 1.0 O F:HOH27 2.3 25.0 1.0 OP1 E:DA14 2.3 34.5 1.0 OD2 B:ASP344 2.4 26.7 1.0 O B:HOH85 2.5 29.8 1.0 O B:ASP444 2.6 29.6 1.0 CG B:ASP344 3.4 25.6 1.0 P F:DC17 3.5 34.4 1.0 C B:ASP444 3.6 30.4 1.0 O F:HOH36 3.6 45.9 1.0 P E:DA14 3.7 33.7 1.0 OD1 B:ASP344 3.7 31.2 1.0 OP2 F:DC17 4.0 35.0 1.0 CA B:ASP444 4.1 29.8 1.0 O3' E:DA13 4.1 33.0 1.0 O5' F:DC17 4.2 35.3 1.0 NZ B:LYS523 4.3 42.6 1.0 C4' F:DC17 4.4 39.4 1.0 O B:MET443 4.5 27.9 1.0 C5' E:DA14 4.5 31.9 1.0 C4' E:DA14 4.5 32.2 1.0 O5' E:DA14 4.6 31.7 1.0 OP2 E:DA14 4.7 35.4 1.0 O3' F:DT16 4.7 32.9 1.0 N B:ASP445 4.7 28.8 1.0 CD1 B:TRP362 4.7 25.8 1.0 CB B:ASP344 4.8 25.6 1.0 NE1 B:TRP362 4.8 26.7 1.0 C5' F:DC17 4.9 38.9 1.0 O3' F:DC17 5.0 43.3 1.0

Calcium binding site 6 out of 6 in the The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Homing Endonuclease I-Scei Bound to Its Dna Recognition Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca537 b:34.0 occ:1.00 O B:HOH141 2.1 36.7 1.0 OD1 B:ASP445 2.2 33.1 1.0 OP2 E:DC15 2.2 37.4 1.0 OP2 F:DC17 2.5 35.0 1.0 OD1 B:ASP344 2.5 31.2 1.0 O B:GLY343 2.7 30.3 1.0 CG B:ASP445 3.2 30.8 1.0 O B:HOH23 3.3 30.8 1.0 C B:GLY343 3.3 27.4 1.0 P E:DC15 3.6 34.9 1.0 OD2 B:ASP445 3.7 33.5 1.0 CG B:ASP344 3.7 25.6 1.0 N B:ASP344 4.0 26.9 1.0 P F:DC17 4.0 34.4 1.0 O3' E:DA14 4.0 35.9 1.0 CA B:GLY343 4.1 27.9 1.0 CA B:ASP344 4.1 24.3 1.0 O B:HOH86 4.3 34.4 1.0 CB B:ASP445 4.4 30.2 1.0 O B:ASN463 4.4 24.6 1.0 OP1 E:DC15 4.5 36.5 1.0 O5' F:DT16 4.5 38.6 1.0 CB B:ASP344 4.6 25.6 1.0 O5' F:DC17 4.6 35.3 1.0 CA B:ASP445 4.6 28.9 1.0 O5' E:DC15 4.6 37.0 1.0 OD2 B:ASP344 4.6 26.7 1.0 N B:ASP445 4.8 28.8 1.0 OP1 F:DC17 4.8 34.8 1.0 C4' F:DT16 4.9 31.7 1.0 O3' F:DT16 4.9 32.9 1.0 C B:ASP444 4.9 30.4 1.0 O B:ASP444 4.9 29.6 1.0

C.M.Moure, F.S.Gimble, F.A.Quiocho. The Crystal Structure of the Gene Targeting Homing Endonuclease I-Scei Reveals the Origins of Its Target Site Specificity J.Mol.Biol. V. 334 685 2003.
ISSN: ISSN 0022-2836
PubMed: 14636596
DOI: 10.1016/J.JMB.2003.09.068