Calcium in PDB 4aqu: Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium

The structure of Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium, PDB code: 4aqu was solved by J.Valton, F.Daboussi, S.Leduc, P.Redondo, R.Macmaster, R.Molina, G.Montoya, P.Duchateau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.801 / 2.30
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.580, 45.355, 172.331, 90.00, 90.00, 90.00
R / Rfree (%)	19.59 / 24.87

The binding sites of Calcium atom in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium (pdb code 4aqu). 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 I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium, PDB code: 4aqu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium


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 I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1154 b:22.3 occ:1.00 OP1 D:5CM514 2.2 28.2 1.0 OP2 C:DG415 2.3 27.8 1.0 O A:HOH2052 2.4 23.9 1.0 OD2 A:ASP20 2.4 23.8 1.0 O B:GLY219 2.4 25.7 1.0 O A:HOH2005 2.5 23.1 1.0 OD1 A:ASP20 2.5 30.5 1.0 CG A:ASP20 2.8 17.3 1.0 C B:GLY219 3.5 32.8 1.0 P C:DG415 3.6 26.6 1.0 P D:5CM514 3.7 29.3 1.0 O A:HOH2003 3.7 17.6 1.0 CA B:GLY219 4.0 24.9 1.0 O3' D:DA513 4.1 26.8 1.0 O5' C:DG415 4.1 32.0 1.0 NE2 A:GLN47 4.1 25.1 1.0 O B:ASP218 4.3 23.8 1.0 C5' C:DG415 4.3 36.9 1.0 CB A:ASP20 4.3 20.5 1.0 OP1 C:DG415 4.4 33.6 1.0 OE1 A:GLN47 4.4 29.6 1.0 C5' D:5CM514 4.5 23.0 1.0 O3 B:GOL1354 4.5 48.4 1.0 OP2 D:5CM514 4.6 30.5 1.0 O5' D:5CM514 4.6 30.0 1.0 N B:ASP220 4.6 19.4 1.0 CD A:GLN47 4.7 30.4 1.0 C4' D:5CM514 4.7 36.2 1.0 O3' C:DA414 4.8 27.2 0.8 OD1 B:ASP220 4.8 21.4 1.0 CA B:ASP220 4.9 23.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium


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 I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1156 b:25.5 occ:1.00 OP1 C:DA414 2.3 22.1 1.0 OP2 D:DG515 2.3 20.9 1.0 O A:GLY19 2.3 26.4 1.0 O A:HOH2002 2.4 21.0 1.0 OD2 B:ASP220 2.4 17.8 1.0 O A:HOH2001 2.5 16.9 1.0 OD1 B:ASP220 2.6 21.4 1.0 CG B:ASP220 2.9 22.3 1.0 C A:GLY19 3.4 26.0 1.0 O A:HOH2003 3.5 17.6 1.0 P D:DG515 3.6 25.2 1.0 P C:DA414 3.6 22.4 1.0 CA A:GLY19 3.9 19.2 1.0 O3' C:DG413 4.0 24.4 0.9 O5' D:DG515 4.1 23.3 1.0 NE2 B:GLN247 4.2 17.3 1.0 O A:ASP18 4.3 24.1 1.0 CB B:ASP220 4.4 18.3 1.0 OP1 D:DG515 4.4 26.7 1.0 C4' C:DA414 4.5 29.7 1.0 C5' C:DA414 4.5 23.5 1.0 OE1 B:GLN247 4.5 19.7 1.0 N A:ASP20 4.5 17.8 1.0 C5' D:DG515 4.5 23.2 1.0 O1 A:GOL1155 4.6 50.1 1.0 O5' C:DA414 4.6 18.5 0.8 OP2 C:DA414 4.7 19.3 1.0 CD B:GLN247 4.8 21.4 1.0 O3' D:5CM514 4.8 25.2 1.0 OD1 A:ASP20 4.9 30.5 1.0 CA A:ASP20 4.9 23.5 1.0 N A:GLY19 5.0 25.2 1.0

J.Valton, F.Daboussi, S.Leduc, R.Molina, P.Redondo, R.Macmaster, G.Montoya, P.Duchateau. 5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases. J.Biol.Chem. V. 287 30139 2012.
ISSN: ISSN 0021-9258
PubMed: 22740697
DOI: 10.1074/JBC.M112.379966