Calcium in PDB 2ex5: Group I Intron-Encoded Homing Endonuclease I-Ceui Complexed with Dna

The structure of Group I Intron-Encoded Homing Endonuclease I-Ceui Complexed with Dna, PDB code: 2ex5 was solved by P.C.Spiegel, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.234, 69.176, 169.414, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 23.1

The binding sites of Calcium atom in the Group I Intron-Encoded Homing Endonuclease I-Ceui Complexed with Dna (pdb code 2ex5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Group I Intron-Encoded Homing Endonuclease I-Ceui Complexed with Dna, PDB code: 2ex5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Group I Intron-Encoded Homing Endonuclease I-Ceui Complexed with 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 Intron-Encoded Homing Endonuclease I-Ceui Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca802 b:36.7 occ:1.00 OP2 Y:DG716 2.2 36.2 1.0 OP2 X:DG616 2.2 37.6 1.0 OE1 A:GLU66 2.4 37.9 1.0 OE2 B:GLU66 2.4 38.8 1.0 OE1 B:GLU66 2.4 31.9 1.0 CD B:GLU66 2.7 36.6 1.0 O3' X:DA615 3.0 38.5 1.0 O3' Y:DG715 3.1 34.9 1.0 O A:GLY65 3.2 35.6 1.0 P X:DG616 3.2 39.3 1.0 P Y:DG716 3.2 38.1 1.0 CD A:GLU66 3.3 35.7 1.0 O B:GLY65 3.8 32.7 1.0 O A:HOH1001 3.8 37.3 1.0 OE2 A:GLU66 3.9 40.4 1.0 O Y:HOH1002 3.9 21.9 1.0 O5' Y:DG716 3.9 30.6 1.0 C A:GLY65 4.0 33.4 1.0 C3' Y:DG715 4.1 33.5 1.0 O5' X:DG616 4.1 40.0 1.0 C3' X:DA615 4.1 39.4 1.0 CG A:GLU66 4.2 33.4 1.0 CG B:GLU66 4.2 34.2 1.0 C B:GLY65 4.3 32.1 1.0 OP1 X:DG616 4.4 42.3 1.0 CA A:GLU66 4.5 29.2 1.0 OP1 Y:DG716 4.5 37.5 1.0 C4' X:DA615 4.5 41.5 1.0 C4' Y:DG715 4.5 37.5 1.0 N A:GLU66 4.6 31.1 1.0 CA A:GLY65 4.7 33.5 1.0 CB A:GLU66 4.8 30.8 1.0 CA B:GLU66 4.8 31.7 1.0 CA B:GLY65 4.9 29.6 1.0 CB B:GLU66 4.9 31.6 1.0 N B:GLU66 4.9 31.5 1.0 O5' X:DA615 5.0 48.5 1.0

Calcium binding site 2 out of 3 in the Group I Intron-Encoded Homing Endonuclease I-Ceui Complexed with 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 Intron-Encoded Homing Endonuclease I-Ceui Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:34.0 occ:1.00 O A:HOH1077 2.3 24.1 1.0 O X:HOH1097 2.4 33.8 1.0 O A:HOH1003 2.5 18.0 1.0 O A:HOH1078 2.6 27.2 1.0 OD1 A:ASP86 2.6 30.7 1.0 OD2 A:ASP86 2.7 31.6 1.0 O A:HOH1137 2.7 58.5 1.0 CG A:ASP86 3.0 31.8 1.0 O A:HOH1095 4.2 31.9 1.0 N7 X:DA605 4.2 35.5 1.0 C8 X:DA605 4.3 38.0 1.0 O A:ASP128 4.3 28.5 1.0 N7 X:DA606 4.4 36.3 1.0 CB A:ASP128 4.4 29.6 1.0 OP2 X:DA605 4.5 43.0 1.0 N6 X:DA606 4.5 27.9 1.0 O A:PRO87 4.6 24.4 1.0 CB A:ASP86 4.6 30.6 1.0 OD1 A:ASP128 4.7 32.6 1.0 CG A:ASP128 4.8 31.5 1.0

Calcium binding site 3 out of 3 in the Group I Intron-Encoded Homing Endonuclease I-Ceui Complexed with 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 Intron-Encoded Homing Endonuclease I-Ceui Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:51.1 occ:1.00 O Y:HOH1096 2.4 48.6 1.0 O B:HOH1173 2.6 32.4 1.0 O Y:HOH1103 2.7 37.7 1.0 OD2 B:ASP86 2.7 43.4 1.0 OD1 B:ASP86 2.9 43.8 1.0 O X:HOH1175 3.0 48.5 1.0 CG B:ASP86 3.2 43.2 1.0 O6 X:DG620 4.2 53.4 1.0 OD2 B:ASP128 4.3 48.4 1.0 NZ B:LYS74 4.3 48.4 1.0 O B:HOH1081 4.5 37.1 1.0 N4 Y:DC707 4.5 43.9 1.0 O6 Y:DG706 4.5 49.6 1.0 O Y:HOH1142 4.6 45.7 1.0 CB B:ASP128 4.6 40.6 1.0 O B:HOH1177 4.6 41.6 1.0 OE1 B:GLU88 4.7 40.2 1.0 CB B:ASP86 4.7 43.5 1.0 O X:HOH1093 4.7 57.9 1.0 N7 Y:DG706 4.7 48.0 1.0 CG B:ASP128 4.8 45.6 1.0 C5 Y:DC705 4.8 39.1 1.0 CE B:LYS74 5.0 51.0 1.0

P.C.Spiegel, B.Chevalier, D.Sussman, M.Turmel, C.Lemieux, B.L.Stoddard. The Structure of I-Ceui Homing Endonuclease: Evolving Asymmetric Dna Recognition From A Symmetric Protein Scaffold. Structure V. 14 869 2006.
ISSN: ISSN 0969-2126
PubMed: 16698548
DOI: 10.1016/J.STR.2006.03.009