Magnesium in PDB 6fb8: Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium

The structure of Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium, PDB code: 6fb8 was solved by R.Molina, J.Prieto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.42 / 2.45
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	79.480, 79.480, 125.760, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium (pdb code 6fb8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium, PDB code: 6fb8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region 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 the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:28.4 occ:1.00 O C:HOH607 2.0 47.5 1.0 OD2 A:ASP20 2.1 45.6 1.0 O B:GLY219 2.2 40.8 1.0 OP1 D:DC614 2.2 35.0 1.0 O B:HOH511 2.3 43.0 1.0 OP2 C:DG515 2.3 46.8 1.0 CG A:ASP20 2.8 42.6 1.0 OD1 A:ASP20 2.8 46.2 1.0 C B:GLY219 3.2 44.1 1.0 P C:DG515 3.6 51.2 1.0 O B:HOH501 3.6 29.8 1.0 P D:DC614 3.6 40.6 1.0 CA B:GLY219 3.8 43.0 1.0 OP1 C:DG515 4.0 46.1 1.0 NE2 A:GLN47 4.1 36.2 1.0 O B:ASP218 4.1 39.0 1.0 O3' D:DA613 4.2 45.1 1.0 O5' C:DG515 4.2 48.3 1.0 C5' D:DC614 4.3 47.4 1.0 CB A:ASP20 4.3 36.5 1.0 OE1 A:GLN47 4.3 40.4 1.0 N B:ASP220 4.4 42.3 1.0 O1 B:PGO402 4.4 59.2 1.0 OD1 B:ASP220 4.4 45.9 1.0 C5' C:DG515 4.4 46.5 1.0 O5' D:DC614 4.5 41.3 1.0 C4' D:DC614 4.5 47.7 1.0 CD A:GLN47 4.7 43.0 1.0 OP2 D:DC614 4.7 47.1 1.0 O3' C:DC514 4.8 54.9 1.0 N B:GLY219 4.8 41.5 1.0 CA B:ASP220 4.9 41.0 1.0 C B:ASP218 4.9 47.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region 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 the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:26.7 occ:1.00 OP1 C:DC514 2.2 43.1 1.0 OD2 B:ASP220 2.2 39.8 1.0 OP2 D:DG615 2.2 46.3 1.0 O A:GLY19 2.3 39.1 1.0 O A:HOH311 2.3 41.9 1.0 O D:HOH816 2.4 45.8 1.0 CG B:ASP220 3.0 41.3 1.0 OD1 B:ASP220 3.1 45.9 1.0 C A:GLY19 3.4 44.4 1.0 P D:DG615 3.5 50.8 1.0 P C:DC514 3.6 44.7 1.0 O B:HOH501 3.6 29.8 1.0 CA A:GLY19 4.0 40.7 1.0 OP1 D:DG615 4.1 46.4 1.0 O5' D:DG615 4.1 46.9 1.0 O3' C:DA513 4.1 48.0 1.0 O A:ASP18 4.1 45.8 1.0 NE2 B:GLN247 4.3 42.5 1.0 C5' C:DC514 4.4 45.0 1.0 C5' D:DG615 4.4 47.3 1.0 OE1 B:GLN247 4.4 41.8 1.0 CB B:ASP220 4.5 37.8 1.0 O5' C:DC514 4.5 45.8 1.0 N A:ASP20 4.6 39.2 1.0 OP2 C:DC514 4.6 48.4 1.0 O1 A:PGO202 4.6 58.2 1.0 C4' C:DC514 4.6 46.8 1.0 OD1 A:ASP20 4.6 46.2 1.0 O3' D:DC614 4.7 48.7 1.0 CD B:GLN247 4.7 46.7 1.0 CA A:ASP20 5.0 37.5 1.0 C A:ASP18 5.0 46.0 1.0 N A:GLY19 5.0 41.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region 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 the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:49.7 occ:1.00 O A:HOH326 2.0 55.0 1.0 O A:ALA134 2.3 56.5 1.0 O A:HOH301 2.3 53.9 1.0 O A:HOH322 2.5 56.5 1.0 O A:HOH304 2.6 53.5 1.0 O A:ASN136 2.7 54.1 1.0 C A:ALA134 3.5 52.8 1.0 C A:ASN136 3.8 54.0 1.0 C A:LEU135 4.2 52.0 1.0 O A:LEU135 4.3 60.3 1.0 CA A:ALA134 4.4 66.5 1.0 N A:ASN136 4.4 48.6 1.0 NE2 B:GLN250 4.5 59.1 1.0 N A:LEU135 4.5 48.4 1.0 O A:ALA133 4.5 58.9 1.0 CA A:LEU135 4.5 55.0 1.0 CA A:ASP137 4.6 54.3 1.0 N A:ASP137 4.6 53.6 1.0 OD1 A:ASP137 4.6 56.7 1.0 CA A:ASN136 4.7 53.7 1.0 N A:SER138 4.9 53.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region 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 4 of Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with An Altered Version of Its Target Dna at 5NNN Region in the Presence of Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:50.7 occ:1.00 O B:HOH505 2.4 64.6 1.0 O A:HOH325 2.4 63.4 1.0 O B:ALA334 2.4 49.5 1.0 O B:HOH524 2.5 61.6 1.0 O B:HOH517 2.7 62.3 1.0 O B:ASN336 2.7 59.9 1.0 C B:ALA334 3.6 55.3 1.0 C B:ASN336 3.8 55.8 1.0 C B:LEU335 4.3 54.6 1.0 O B:LEU335 4.3 56.0 1.0 NE2 A:GLN50 4.4 61.7 1.0 O B:ALA333 4.4 60.7 1.0 CA B:ASP337 4.4 58.4 1.0 N B:ASN336 4.5 53.0 1.0 N B:ASP337 4.5 57.6 1.0 CA B:ALA334 4.5 65.5 1.0 N B:LEU335 4.6 51.4 1.0 OD1 B:ASP337 4.7 64.7 1.0 N B:SER338 4.7 58.8 1.0 CA B:LEU335 4.7 55.1 1.0 CA B:ASN336 4.8 55.0 1.0

J.Prieto, P.Redondo, B.Lopez-Mendez, M.D'abramo, N.Merino, F.J.Blanco, P.Duchateau, G.Montoya, R.Molina. Understanding the Indirect Dna Read-Out Specificity of I-Crei Meganuclease. Sci Rep V. 8 10286 2018.
ISSN: ESSN 2045-2322
PubMed: 29980759
DOI: 10.1038/S41598-018-28599-0