Calcium in PDB 3ool: I-Scei Complexed with C/G+4 Dna Substrate

The structure of I-Scei Complexed with C/G+4 Dna Substrate, PDB code: 3ool was solved by R.Joshi, J.-H.Chen, B.L.Golden, F.S.Gimble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.79 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.184, 49.938, 63.360, 90.00, 107.54, 90.00
R / Rfree (%)	24.6 / 29.4

The binding sites of Calcium atom in the I-Scei Complexed with C/G+4 Dna Substrate (pdb code 3ool). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the I-Scei Complexed with C/G+4 Dna Substrate, PDB code: 3ool:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the I-Scei Complexed with C/G+4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of I-Scei Complexed with C/G+4 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca236 b:24.5 occ:1.00 OP1 C:DA14 2.1 26.0 1.0 OP1 D:DC17 2.3 27.1 1.0 OD2 A:ASP44 2.3 30.6 1.0 O A:ASP144 2.3 25.5 1.0 O A:HOH243 2.4 2.0 1.0 CG A:ASP44 3.2 29.6 1.0 OD1 A:ASP44 3.4 31.1 1.0 P D:DC17 3.4 28.5 1.0 C A:ASP144 3.5 25.8 1.0 P C:DA14 3.6 26.4 1.0 OP2 D:DC17 3.8 28.6 1.0 C5' C:DA14 4.0 24.7 1.0 O5' D:DC17 4.0 28.6 1.0 CA A:ASP144 4.1 25.5 1.0 O3' C:DA13 4.2 26.6 1.0 O5' C:DA14 4.3 26.6 1.0 NE1 A:TRP62 4.4 29.5 1.0 C5' D:DC17 4.5 28.0 1.0 NZ A:LYS223 4.5 29.8 1.0 C4' C:DA14 4.5 24.1 1.0 O A:MET143 4.6 26.6 1.0 CD1 A:TRP62 4.6 29.2 1.0 N A:ASP145 4.6 26.2 1.0 CB A:ASP44 4.6 27.4 1.0 OP2 C:DA14 4.7 28.2 1.0 O3' D:DT16 4.7 27.9 1.0 CA A:ASP145 4.9 26.8 1.0 CB A:ASP144 5.0 25.2 1.0

Calcium binding site 2 out of 3 in the I-Scei Complexed with C/G+4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of I-Scei Complexed with C/G+4 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca237 b:46.2 occ:1.00 OP2 C:DC15 2.3 32.2 1.0 O A:HOH253 2.4 5.3 1.0 O D:HOH31 2.5 11.4 1.0 O A:GLY43 2.6 27.3 1.0 OD1 A:ASP145 2.7 29.1 1.0 OD1 A:ASP44 3.0 31.1 1.0 C A:GLY43 3.3 26.8 1.0 P C:DC15 3.5 30.1 1.0 CG A:ASP145 3.5 28.0 1.0 OD2 A:ASP145 3.7 30.7 1.0 OP1 C:DC15 3.8 31.8 1.0 N A:ASP44 4.1 26.8 1.0 CA A:GLY43 4.1 26.8 1.0 CA A:ASP44 4.1 27.2 1.0 CG A:ASP44 4.2 29.6 1.0 OP2 D:DT16 4.2 28.8 1.0 O A:HOH241 4.4 9.4 1.0 O A:ASN163 4.5 24.0 1.0 O3' C:DA14 4.5 28.7 1.0 O5' C:DC15 4.6 28.8 1.0 C5' C:DC15 4.8 28.1 1.0 OP2 D:DC17 4.8 28.6 1.0 CB A:ASP44 4.8 27.4 1.0 O A:LEU42 4.8 27.0 1.0 CB A:ASP145 4.9 27.0 1.0 OP1 D:DC17 5.0 27.1 1.0

Calcium binding site 3 out of 3 in the I-Scei Complexed with C/G+4 Dna Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of I-Scei Complexed with C/G+4 Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca26 b:26.6 occ:1.00 OP1 C:DC15 2.2 31.8 1.0 OP1 D:DT16 2.4 27.4 1.0 O D:HOH29 2.4 3.6 1.0 O C:HOH31 2.5 8.7 1.0 O C:HOH33 2.6 3.6 1.0 P C:DC15 3.6 30.1 1.0 P D:DT16 3.7 27.9 1.0 O4' D:DA15 3.9 25.1 1.0 O3' C:DA14 4.0 28.7 1.0 OP2 D:DT16 4.1 28.8 1.0 O4' C:DC15 4.2 26.4 1.0 C4' D:DA15 4.3 26.4 1.0 O5' C:DC15 4.3 28.8 1.0 O4' D:DT16 4.3 28.6 1.0 C1' D:DA15 4.4 26.8 1.0 C4' C:DC15 4.5 27.1 1.0 C4' D:DT16 4.5 28.6 1.0 N3 D:DA15 4.6 27.0 1.0 O C:HOH30 4.6 18.1 1.0 O3' D:DA15 4.7 29.0 1.0 OP2 C:DC15 4.7 32.2 1.0 O5' D:DT16 4.8 29.3 1.0 O2 D:DT14 4.8 25.5 1.0 C5' C:DC15 4.8 28.1 1.0 N3 C:DA14 5.0 20.1 1.0

R.Joshi, K.K.Ho, K.Tenney, J.H.Chen, B.L.Golden, F.S.Gimble. Evolution of I-Scei Homing Endonucleases with Increased Dna Recognition Site Specificity. J.Mol.Biol. V. 405 185 2011.
ISSN: ISSN 0022-2836
PubMed: 21029741
DOI: 10.1016/J.JMB.2010.10.029