Manganese in PDB 6fb7: Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese

The structure of Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese, PDB code: 6fb7 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)	49.02 / 2.69
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.504, 169.153, 49.015, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.1

The binding sites of Manganese atom in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese (pdb code 6fb7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese, PDB code: 6fb7:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:39.5 occ:1.00 O3' F:DC614 2.1 36.0 1.0 OD1 A:ASP20 2.1 29.5 1.0 OD1 B:ASP20 2.2 35.6 1.0 OP1 G:DG615 2.2 25.5 1.0 OP2 E:DG515 2.3 32.2 1.0 O3' D:DC514 2.5 37.8 1.0 C3' F:DC614 3.1 34.3 1.0 CG A:ASP20 3.1 28.8 1.0 P G:DG615 3.3 31.8 1.0 CG B:ASP20 3.3 33.9 1.0 C3' D:DC514 3.5 37.3 1.0 OD2 A:ASP20 3.5 31.7 1.0 O5' G:DG615 3.5 25.3 1.0 P E:DG515 3.6 32.5 1.0 OP3 G:DG615 3.6 36.1 1.0 C4' F:DC614 3.8 33.7 1.0 O B:GLY19 3.9 38.9 1.0 MN A:MN202 3.9 50.6 1.0 MN A:MN203 4.0 56.4 1.0 OD2 B:ASP20 4.0 35.9 1.0 O5' E:DG515 4.0 29.7 1.0 C4' D:DC514 4.1 39.3 1.0 OP1 E:DG515 4.3 38.6 1.0 O A:GLY19 4.3 34.5 1.0 C2' F:DC614 4.4 35.4 1.0 CB B:ASP20 4.4 29.5 1.0 CA B:ASP20 4.4 34.6 1.0 CB A:ASP20 4.5 25.8 1.0 C B:GLY19 4.5 38.4 1.0 OP2 G:DG615 4.6 41.3 1.0 OP3 E:DG515 4.7 35.1 1.0 OP1 D:DC514 4.7 35.1 1.0 CA A:ASP20 4.7 29.4 1.0 C A:GLY19 4.8 32.6 1.0 C5' F:DC614 4.8 36.0 1.0 C2' D:DC514 4.8 39.7 1.0 N B:ASP20 4.8 38.2 1.0 C1' F:DC614 4.9 36.8 1.0 O4' F:DC614 4.9 33.5 1.0 C5' G:DG615 4.9 29.9 1.0 C5' D:DC514 4.9 43.8 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:50.6 occ:1.00 O A:HOH309 2.1 35.9 1.0 OP1 F:DC614 2.2 28.0 1.0 OP2 E:DG515 2.2 32.2 1.0 OD2 B:ASP20 2.2 35.9 1.0 OP3 E:DG515 2.3 35.1 1.0 O A:GLY19 2.3 34.5 1.0 P E:DG515 2.7 32.5 1.0 CG B:ASP20 3.1 33.9 1.0 OD1 B:ASP20 3.3 35.6 1.0 C A:GLY19 3.3 32.6 1.0 P F:DC614 3.6 34.6 1.0 O5' E:DG515 3.6 29.7 1.0 CA A:GLY19 3.8 31.8 1.0 MN A:MN201 3.9 39.5 1.0 O E:HOH602 3.9 40.1 1.0 OP1 E:DG515 4.0 38.6 1.0 OD1 A:ASP20 4.0 29.5 1.0 O3' F:DA613 4.1 31.9 1.0 O A:ASP18 4.1 35.0 1.0 NE2 B:GLN47 4.2 30.2 1.0 C5' F:DC614 4.3 36.0 1.0 C4' F:DC614 4.3 33.7 1.0 OE1 B:GLN47 4.3 31.7 1.0 C5' E:DG515 4.4 28.0 1.0 N A:ASP20 4.4 30.0 1.0 O5' F:DC614 4.5 37.5 1.0 CB B:ASP20 4.5 29.5 1.0 OP2 F:DC614 4.6 40.8 1.0 CD B:GLN47 4.7 30.8 1.0 O3' F:DC614 4.8 36.0 1.0 CA A:ASP20 4.8 29.4 1.0 C3' F:DC614 4.9 34.3 1.0 N A:GLY19 4.9 32.9 1.0 C A:ASP18 4.9 34.2 1.0 NH2 B:ARG51 5.0 52.6 1.0 O3' D:DC514 5.0 37.8 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the I-Crei Homing Endonuclease D75N Variant in Complex with Its Target Dna in the Presence of Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:56.4 occ:1.00 OP1 G:DG615 2.0 25.5 1.0 OP1 D:DC514 2.1 35.1 1.0 OD2 A:ASP20 2.2 31.7 1.0 O A:HOH302 2.2 38.8 1.0 O B:GLY19 2.3 38.9 1.0 OP2 G:DG615 2.4 41.3 1.0 P G:DG615 2.6 31.8 1.0 CG A:ASP20 3.3 28.8 1.0 C B:GLY19 3.3 38.4 1.0 P D:DC514 3.5 37.1 1.0 O5' G:DG615 3.6 25.3 1.0 OD1 A:ASP20 3.8 29.5 1.0 OP3 G:DG615 3.8 36.1 1.0 CA B:GLY19 3.8 36.7 1.0 MN A:MN201 4.0 39.5 1.0 O B:ASP18 4.1 42.3 1.0 O3' D:DA513 4.1 31.9 1.0 OE1 A:GLN47 4.1 29.5 1.0 C5' G:DG615 4.2 29.9 1.0 NE2 A:GLN47 4.4 26.5 1.0 OP2 D:DC514 4.4 34.8 1.0 N B:ASP20 4.5 38.2 1.0 C5' D:DC514 4.5 43.8 1.0 CB A:ASP20 4.6 25.8 1.0 O5' D:DC514 4.6 49.1 1.0 OD1 B:ASP20 4.6 35.6 1.0 CD A:GLN47 4.6 30.1 1.0 C4' D:DC514 4.7 39.3 1.0 N B:GLY19 4.8 39.8 1.0 C B:ASP18 4.9 41.4 1.0 CA B:ASP20 4.9 34.6 1.0 NH2 A:ARG51 5.0 65.4 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