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

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 Magnesium, PDB code: 4aqx 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)	45.793 / 2.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.839, 71.401, 179.054, 90.00, 90.00, 90.00
R / Rfree (%)	20.15 / 24.18

The binding sites of Magnesium 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 Magnesium (pdb code 4aqx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium, PDB code: 4aqx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1525 b:31.7 occ:1.00 OP1 F:DG615 2.1 34.7 1.0 O3' C:DA514 2.1 34.5 0.9 O3' E:5CM614 2.1 38.7 1.0 OP2 D:DG515 2.1 35.3 0.9 OD1 A:ASP20 2.2 34.9 1.0 OD1 B:ASP20 2.2 35.8 1.0 C3' E:5CM614 3.2 43.6 1.0 C3' C:DA514 3.3 35.1 0.9 P F:DG615 3.3 34.9 1.0 CG A:ASP20 3.3 38.0 1.0 P D:DG515 3.3 35.8 0.9 CG B:ASP20 3.4 39.2 1.0 O5' F:DG615 3.6 38.0 1.0 O5' D:DG515 3.7 28.7 0.9 MG D:MG1526 3.8 30.7 1.0 OD2 A:ASP20 3.8 31.5 1.0 O C:HOH2014 3.9 40.8 1.0 OP3 F:DG615 3.9 28.4 1.0 MG F:MG1625 3.9 40.2 1.0 C4' E:5CM614 3.9 36.4 1.0 OP1 D:DG515 3.9 33.9 0.9 OD2 B:ASP20 3.9 31.7 1.0 O A:GLY19 4.0 30.9 1.0 C4' C:DA514 4.0 30.1 0.9 O B:GLY19 4.0 32.6 1.0 O C:HOH2016 4.2 42.9 1.0 C2' E:5CM614 4.4 41.3 1.0 C2' C:DA514 4.5 27.7 0.9 OP2 F:DG615 4.5 37.4 1.0 OP3 D:DG515 4.5 29.1 0.9 CB A:ASP20 4.5 29.6 1.0 CB B:ASP20 4.6 35.3 1.0 C A:GLY19 4.6 35.6 1.0 CA A:ASP20 4.6 33.9 1.0 CA B:ASP20 4.6 30.2 1.0 C B:GLY19 4.7 34.3 1.0 C5' E:5CM614 4.8 37.0 1.0 OP2 E:5CM614 4.8 37.9 1.0 OP1 C:DA514 4.8 33.5 0.9 C1' E:5CM614 4.9 43.6 1.0 N A:ASP20 4.9 30.1 1.0 C5' C:DA514 4.9 31.1 0.9 C5' F:DG615 5.0 29.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1526 b:30.7 occ:1.00 OD2 B:ASP20 2.0 31.7 1.0 O A:GLY19 2.1 30.9 1.0 OP2 E:5CM614 2.1 37.9 1.0 OP2 D:DG515 2.1 35.3 0.9 O A:HOH2004 2.1 33.0 1.0 OP3 D:DG515 2.3 29.1 0.9 P D:DG515 2.7 35.8 0.9 CG B:ASP20 2.9 39.2 1.0 C A:GLY19 3.2 35.6 1.0 OD1 B:ASP20 3.2 35.8 1.0 P E:5CM614 3.6 41.3 1.0 O5' D:DG515 3.7 28.7 0.9 CA A:GLY19 3.7 36.1 1.0 MG D:MG1525 3.8 31.7 1.0 O A:HOH2043 3.9 46.7 1.0 OP1 D:DG515 3.9 33.9 0.9 O3' E:DA613 4.1 36.5 0.8 C5' E:5CM614 4.2 37.0 1.0 NE2 B:GLN47 4.2 34.1 1.0 OE1 B:GLN47 4.2 42.6 1.0 OD1 A:ASP20 4.3 34.9 1.0 O A:ASP18 4.3 39.4 1.0 N A:ASP20 4.3 30.1 1.0 C5' D:DG515 4.3 31.6 0.9 CB B:ASP20 4.3 35.3 1.0 O5' E:5CM614 4.4 42.0 1.0 C4' E:5CM614 4.4 36.4 1.0 OP1 E:5CM614 4.5 47.2 1.0 CD B:GLN47 4.6 42.8 1.0 O A:HOH2051 4.6 48.4 1.0 O3' E:5CM614 4.7 38.7 1.0 CA A:ASP20 4.8 33.9 1.0 C3' E:5CM614 4.8 43.6 1.0 N A:GLY19 4.9 34.1 1.0 O3' C:DA514 4.9 34.5 0.9

Magnesium binding site 3 out of 3 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1625 b:40.2 occ:1.00 OD2 A:ASP20 2.1 31.5 1.0 OP1 C:DA514 2.1 33.5 0.9 O A:HOH2006 2.1 28.4 1.0 OP1 F:DG615 2.2 34.7 1.0 OP2 F:DG615 2.2 37.4 1.0 O B:GLY19 2.3 32.6 1.0 P F:DG615 2.6 34.9 1.0 CG A:ASP20 3.1 38.0 1.0 C B:GLY19 3.4 34.3 1.0 OD1 A:ASP20 3.4 34.9 1.0 P C:DA514 3.4 27.4 0.9 O B:HOH2031 3.6 41.1 1.0 O5' F:DG615 3.7 38.0 1.0 OP3 F:DG615 3.8 28.4 1.0 O3' C:DG513 3.9 26.2 0.9 CA B:GLY19 3.9 33.7 1.0 MG D:MG1525 3.9 31.7 1.0 OE1 A:GLN47 4.1 36.1 1.0 O B:ASP18 4.2 27.8 1.0 NE2 A:GLN47 4.2 33.1 1.0 C5' C:DA514 4.2 31.1 0.9 C4' C:DA514 4.4 30.1 0.9 OD1 B:ASP20 4.4 35.8 1.0 O5' C:DA514 4.4 34.2 0.9 C5' F:DG615 4.4 29.4 1.0 CB A:ASP20 4.4 29.6 1.0 OP2 C:DA514 4.5 30.2 0.9 N B:ASP20 4.5 35.6 1.0 CD A:GLN47 4.6 36.7 1.0 O3' C:DA514 4.6 34.5 0.9 O B:HOH2038 4.6 39.7 1.0 C3' C:DA514 4.8 35.1 0.9 CA B:ASP20 4.9 30.2 1.0 N B:GLY19 5.0 33.5 1.0 O3' E:5CM614 5.0 38.7 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