Calcium in PDB 5a72: Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca

The structure of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca, PDB code: 5a72 was solved by R.Molina, P.Redondo, B.Lopezmendez, M.Villate, N.Merino, F.J.Blanco, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.105 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.179, 94.210, 51.340, 90.00, 104.83, 90.00
R / Rfree (%)	16.14 / 23.31

The binding sites of Calcium atom in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca (pdb code 5a72). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca, PDB code: 5a72:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1163 b:29.2 occ:1.00 OP1 D:DG615 2.3 33.8 1.0 O B:ALA22 2.4 26.1 1.0 OP1 C:DC514 2.4 36.0 1.0 OD2 A:ASP23 2.4 32.8 1.0 O A:HOH2004 2.5 28.2 1.0 O A:HOH2041 2.9 36.5 1.0 OD1 A:ASP23 3.1 35.8 1.0 CG A:ASP23 3.1 35.8 1.0 C B:ALA22 3.4 26.9 1.0 O A:HOH2003 3.5 36.5 1.0 P C:DC514 3.6 31.9 1.0 P D:DG615 3.6 31.6 1.0 O5' C:DC514 3.7 39.2 1.0 O5' D:DG615 4.0 32.7 1.0 CA B:ALA22 4.0 25.8 1.0 O3' C:DA513 4.2 31.6 1.0 OP2 D:DG615 4.3 28.6 1.0 OE1 A:GLN50 4.4 29.7 1.0 NE2 A:GLN50 4.4 28.2 1.0 N B:ASP23 4.5 28.4 1.0 C4' C:DC514 4.5 30.7 1.0 OD1 B:ASP23 4.5 31.6 1.0 CB A:ASP23 4.6 31.7 1.0 CB B:ALA22 4.7 25.2 1.0 C5' C:DC514 4.7 29.6 1.0 O3' D:DC614 4.7 26.0 1.0 CA B:ASP23 4.8 32.1 1.0 CD A:GLN50 4.9 30.3 1.0 OP2 C:DC514 4.9 33.0 1.0 O3' C:DC514 4.9 30.1 1.0 O B:ASP21 5.0 29.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Ca within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1164 b:33.2 occ:1.00 OP1 D:DC614 2.3 29.3 1.0 O A:ALA22 2.3 26.7 1.0 O A:HOH2001 2.4 30.5 1.0 OP2 C:DG515 2.4 31.8 1.0 OD2 B:ASP23 2.5 35.3 1.0 O A:HOH2002 2.6 32.4 1.0 OD1 B:ASP23 3.1 31.6 1.0 CG B:ASP23 3.2 32.8 1.0 C A:ALA22 3.4 26.5 1.0 O A:HOH2003 3.6 36.5 1.0 P C:DG515 3.7 31.4 1.0 P D:DC614 3.7 33.5 1.0 O5' C:DG515 3.9 31.6 1.0 CA A:ALA22 4.1 26.0 1.0 C5' D:DC614 4.1 29.0 1.0 O3' D:DA613 4.2 26.4 1.0 OE1 B:GLN50 4.3 34.3 1.0 OP1 C:DG515 4.4 30.1 1.0 C4' D:DC614 4.4 30.1 1.0 OD1 A:ASP23 4.4 35.8 1.0 O5' D:DC614 4.5 37.8 1.0 N A:ASP23 4.5 25.7 1.0 NE2 B:GLN50 4.5 32.6 1.0 CB B:ASP23 4.6 32.3 1.0 CA A:ASP23 4.8 30.6 1.0 CB A:ALA22 4.8 25.3 1.0 OP2 D:DC614 4.8 35.2 1.0 O3' C:DC514 4.8 30.1 1.0 CD B:GLN50 4.8 29.3 1.0 O3' D:DC614 4.9 26.0 1.0 O A:ASP21 4.9 27.9 1.0

R.Molina, P.Redondo, B.Lopez-Mendez, M.Villate, N.Merino, F.J.Blanco, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya. Crystal Structure of the Homing Endonuclease I-Cvui Provides A New Template For Genome Modification J.Biol.Chem. V. 290 28727 2015.
ISSN: ISSN 0021-9258
PubMed: 26363068
DOI: 10.1074/JBC.M115.678342